Samtools - [main_samview] fail to read the header

Question

[kstangline]

Hi everyone,

I'm attempting to convert a SAM file to a BAM file using the following command:

samtools view -S -b test.sam > test.bam

However, I'm getting the error [main_samview] fail to read the header (see figure). The figure attached shows the error I'm getting on the top and the contents of the beginning of the SAM file on the bottom. Has anyone seen this before? Is there a simple fix? I'm still new to computational biology, so I'd appreciate any help I can get.

[Ram]

What is the samtools/htslib version you're using? What is the output to samtools view -H filename.sam? Also, please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

[kstangline]

Hello,

I'm using samtools 1.13, htslib 1.13.

This is what I'm getting from samtools view -H:

samtools view -H test.sam

[main_samview] fail to read the header from "test.sam".

Answer 1

[swbarnes2]

The simplest explanation is that your sam has no header. How was it made? If you converted from a bam, you need to include -h to make sure the header isn't omitted.