Header too long for bam format

Question

[selplat21]

I have about 20,000 bam files in a directory called intermediate_bams

These will all have the same @HD and @SQ lines. There are about 860 @SQ lines.

When I try to merge these bams, I get the following output:

samtools merge -h custom_header.sam -o test.bam intermediate_bams/*bam

[E::bam_hdr_write] Header too long for BAM format

Here is the header and tail of my custom_header.sam

@HD VN:1.6  SO:coordinate
@SQ SN:NC_088602.1  LN:212386202
@SQ SN:NC_088603.1  LN:163726572
@SQ SN:NC_088604.1  LN:122092291
@SQ SN:NC_088605.1  LN:78855516
...
@SQ SN:NW_027043814.1   LN:173419
@SQ SN:NW_027043815.1   LN:151889
@SQ SN:NW_027043816.1   LN:151339
@SQ SN:NW_027043817.1   LN:234180
@SQ SN:NW_027043818.1   LN:593964

Answer 1

[Ram]

This error refers to the number of lines in the header, not the length of any single line. See: https://github.com/samtools/samtools/issues/1613

What is the output to wc -l custom_header.sam and command ls -lh custom_header.sam?

[selplat21]

The output of wc -l custom_header.sam is 870

and the output of command ls -lh custom_header.sam is -rw-r--r-- 1 nicolas nicolas 27K Aug 2 21:02 custom_header.sam

The large number corresponds to the large number of scaffolds in my genome. I've never run into this problem before with previous genomes.

[Ram]

That header should not cause a problem. Please add a comment on the issue I have linked to.