sam to bam conversion error, no @SQ lines in the header, missing header?

[efoss]

I have a sam file that I want to convert to a bam file:

samtools view -b -S in.sam > out.bam

I get this error:

[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

My sam file looks perfectly normal to me. Does anyone see what I'm doing wrong?

Thanks.

Eric

[efoss]

To add to my previous post: I also tried the following command but I got the same error message:

samtools view -h -b -S in.sam > out.bam

[BAMseek]

I think you might need to specify a reference file containing the names of the sequences and the total sequence lengths. This is done with the "-t" flag. Here is a description from samtools:

-t FILE
This file is TAB-delimited. Each line must contain the reference name and the length of the reference, one line for each distinct reference;

[maubp]

Or from memory -T can specify a FASTA file of the references.

[swbarnes2]

Or from memory -T can specify a FASTA file of the references.

samtools view doesn't require -T. It works fine without a reference fasta.

Maybe your headers aren't right?

Here's what mine look like:

@SQ SN:SNP_8787 LN:161
@SQ SN:vector LN:13078

[efoss]

samtools view doesn't require -T. It works fine without a reference fasta.

Maybe your headers aren't right?

Here's what mine look like:

@SQ SN:SNP_8787 LN:161
@SQ SN:vector LN:13078

Yes - it was the headers. I see that when I made my sam file, I didn't use the -h option, so then when I went to convert it back to a bam file, I couldn't fix things simply by adding the -h option. I had to go back and remake the sam file with -h and then convert it back to a bam file with -h, and now everything is working fine. Thanks very much, everyone, for the help.

Eric

[prasadg]

Yes - it was the headers. I see that when I made my sam file, I didn't use the -h option, so then when I went to convert it back to a bam file, I couldn't fix things simply by adding the -h option. I had to go back and remake the sam file with -h and then convert it back to a bam file with -h, and now everything is working fine. Thanks very much, everyone, for the help.

Eric

Hey efoss,

I am also facing the same problem. I couldn't undertsood this line of yours "I didn't use the -h option, so then when I went to convert it back to a bam file, I couldn't fix things simply by adding the -h option. I had to go back and remake the sam file with -h" how to did you make same file with -h? Did you use Bwa to create sam file.?

[efoss]

Hey efoss,

I am also facing the same problem. I couldn't undertsood this line of yours "I didn't use the -h option, so then when I went to convert it back to a bam file, I couldn't fix things simply by adding the -h option. I had to go back and remake the sam file with -h" how to did you make same file with -h? Did you use Bwa to create sam file.?

Hi prasadg,

It's been a while, but I think that I created a sam file with samtools' view command and that that command accepts a -h flag, which will create a sam file with appropriate headers.

Eric

[prasadg]

Hi prasadg,

It's been a while, but I think that I created a sam file with samtools' view command and that that command accepts a -h flag, which will create a sam file with appropriate headers.

Eric

Okay . I will look into it . I have the sam file created by bwa. So I was using samtools to convert sam to bam but I am getting same answer as you have got

[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

So I wanted to know how did you do it .

Thanks

[efoss]

Okay . I will look into it . I have the sam file created by bwa. So I was using samtools to convert sam to bam but I am getting same answer as you have got

[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

So I wanted to know how did you do it .

Thanks

Hi prasadg,

Another thing to try if that doesn't work is using the -r option in bwa to add read group information when you create your original alignment file.

Eric

[prasadg]

Hi prasadg,

Another thing to try if that doesn't work is using the -r option in bwa to add read group information when you create your original alignment file.

Eric

I will give it a shot. by -r you mean -R ? cause as I see the alignment options -r is with uppercase. There is no lower case 'r' option.

[efoss]

I will give it a shot. by -r you mean -R ? cause as I see the alignment options -r is with uppercase. There is no lower case 'r' option.

No - I mean -r. Look under sampe and you'll see the option.

Eric

[prasadg]

No - I mean -r. Look under sampe and you'll see the option.

Eric

Thanks alot . It certainly made my day. I certainly was on wrong track .

Really appreciate you replys.

[bbm]

I converted sam file to bam, then removes PCR duplicates, then convert bam to sam. It showed the same error msg:

error msg: [samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

I tried -h option, still didn't work...

[efoss]

Hi bbm,

You might want to try Picard's AddOrReplaceReadGroups:

http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGroups