Missing LN tag

[rhughwhite]

Describe the bug

    [W::sam_hdr_create] Ignored @SQ SN:HLA-C*16:01: : bad or missing LN tag
    [E::sam_hrecs_update_hashes] Header includes @SQ line "HLA-C*16:01:" with no LN: tag
    samtools view: failed to add PG line to the header

Seems like this related to LN tags for different contigs in the reference fasta (GRCh38-BI-20160721/alt-aware/genome.fa).

LN tag for main contigs:
>chr1 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome M5:6aef897c3d6ff0c78aff06ac189178dd AS:GRCh38

But lacking for HLA-specific contig
>HLA-C*16:01:01 HLA00475 3349 bp

Seems odd that this hasn't been an issue before (actually there is an old issue #88). Perhaps samples don't often have reads aligning to these contigs? Other samples in the cohort don't encounter this issue.

Can provide paths to configs, logs etc.

• Actual submission script (python submission script, "nextflow run ...", etc.)
• Sbatch or qsub command and logs if applicable
• Config files
• Path to the working directory
• Any logs produced by the pipeline

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Additional context
Add any other context about the problem here.

[yashpatel6]

The issue doesn't seem related to whether any reads align to that specific contig since the header of the output BAM will contain all contigs listed regardless of alignment and the error comes up when trying to add an @PG line to the header. Similar to #88, it may be worth trying something along the lines of reducing the number of CPUs as the error seen here might be an indirect indication of insufficient memory

[tnyamaguchi]

Not sure if it's related to this issue but we also want to update bwa-mem2 version (released 3 weeks ago) as well for better stability.

https://github.com/bwa-mem2/bwa-mem2/releases/tag/v2.3

[yashpatel6]

Maybe, there's an issue for it already uclahs-cds/docker-BWA-MEM2#9