'no @SQ lines in the header'

Hi all..

I'm stuck at the path where I'm about to call mitochondrial region (ChrM) from the whole genome sequencing data.

I have gone through the fastq, alignment and now I'm going deeper; calling ChrM out (because I'm specifically want to use mitochondrial region only for my study).

What I did was;

1) I have sorted .bam file, the command was like:

samtools sort unsorted_in.bam sorted_out

2) Then I converted the sorted .bam file into .sam. The command was:

samtools view -h file.bam > file.sam

3) After that, I have indexed sorted.bam file and the command was:

samtools index sorted.bam

Everything seems okay until I run the command to call ChrM region. The command for calling ChrM that I have used was this one:

samtools view -h sorted.bam | awk '$3== "chrM" || /[email protected]/' | samtools view -Sb -> chrM.bam.sorted.bam

So, I typed this in the terminal and it appeared:

[email protected]:/srv/disk01/Tools/samtools-0.1.19$ samtools view -h /srv/disk01/Postgraduates/OrangAsli/KS12R/Alignments/KS12R_sorted.bam.bam | awk '$3=="chrM" || /[email protected]/' | samtools view -Sb -> /srv/disk01/Postgraduates/OrangAsli/KS12R/ChrM/KS12R_chrM.bam.sorted.bam
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

I have tried more than twice but it's still the same. What does it mean with 'no @SQ lines in the header?'

I hope you guys can help me. Thank you in advance and glad to hear from you guys soon.

Thanks again,

Best Answer


  • AzlinAzlin Member

    Hi Geraldine,

    Uh-oh. My bad. Thank you for your suggestion :smile:

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