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Samtools Error Message : No @Sq Lines In The Header

I have the same issue with samtools no matter how hard I'm trying to grab the header it just doesn't work .. 

samtools view -H file.bam > header.sam
samtools reheader header.bam header.unique.bam

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

Header.bam has the following content : 

 @SQ     SN:chr1 LN:197195432
 @SQ     SN:chr2 LN:181748087
 @SQ     SN:chr3 LN:159599783
 @SQ     SN:chr4 LN:155630120
 @SQ     SN:chr5 LN:152537259
 @SQ     SN:chr6 LN:149517037
 @SQ     SN:chr7 LN:152524553
 @SQ     SN:chr8 LN:131738871
 @SQ     SN:chr9 LN:124076172
 @SQ     SN:chr10        LN:129993255
 @SQ     SN:chr11        LN:121843856
 @SQ     SN:chr12        LN:121257530
 @SQ     SN:chr13        LN:120284312
 @SQ     SN:chr14        LN:125194864
 @SQ     SN:chr15        LN:103494974
 @SQ     SN:chr16        LN:98319150
 @SQ     SN:chr17        LN:95272651
 @SQ     SN:chr18        LN:90772031
 @SQ     SN:chr19        LN:61342430
 @SQ     SN:chrX LN:166650296
 @SQ     SN:chrY LN:15902555
 @SQ     SN:chrM LN:16299
 @PG     ID:bwa  PN:bwa  VN:0.5.9-r16
 ~
 ~

Interesting thing .. I can view the header of header.bam just by typing 

$ view header-1ips.sam
deleted-post
• 1,290 views • link
updated by Matteo • Matteo • written by madkitty madkitty

Works fine for me. 1) Did you try to output the first command on to your screen to see if everything is right? 2) Are you providing an existing bam file that doesn't have any issues itself?

• 0 views • link
written by Arun Arun

uhm .. is there a way to be sure my bam file doesn't have any issue?

• 1 views • link
written by madkitty madkitty

can you please show the content of : `header.sam' ?

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

I have edited my question with the content of the header.sam file

• 1 views • link
written by madkitty madkitty

sam files are from GSNAP .. we then used samtools to have the bam files.

• 1 views • link
written by madkitty madkitty

1 answer

Hi,

Your header is lacking in the first line (@HD field). Below an example:

@HD VN:1.0 GO:none SO:coordinate

Try to edit the samfile adding the @HD record and let me know.

PS: columns are tab-delimited.

• 0 views • link
written by Matteo • Matteo

I added the @HQ field in the line .. header.sam is still human readable and when I do 

    samtools reheader header.bam header.unique.bam

It says 

open: No such file or directory
[main_reheader] fail to open file header.unique.bam
• 1 views • link
written by madkitty madkitty

It is because you don't have "header.unique.sam" file in the same directory. In the command you say "header.unique.bam" and error is about .sam? I think you are mixing sam and bam extensions.

• 1 views • link
written by Vikas Bansal Vikas Bansal

yeah sorry I mixed up sam and bam in my answer (edited now..), I do have the two files in the same directory which is why I don't understand why it doesn't work..

• 0 views • link
written by madkitty madkitty

In your original post, you have "header.sam" and here now you have "header.bam". Also, in the error, it shows you - fail to open "header.unique.sam" but in input you have "header.unique.bam". Please check all the files in directory and give your commands accordingly.

• 1 views • link
written by Vikas Bansal Vikas Bansal

I'm sorry, I'm just confused whenever I type here, all the extension I use are proper and are BAM format :) The problem come from the syntax ..

• 1 views • link
written by madkitty madkitty

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