PanSN naming issue in pggb fastas

[SquRunner]

I am having an issue with the PanSN naming for pggb fastas and would love any insight.

In preparing for pggb, I am running:

fastix -p "NP117#hap#" 117_Assembly.fasta > 117_shasta_fastix_output.fasta

But run into naming issues with:

pggb -i combined_aligned_contigs.fasta.gz -o pangenome

[pggb] warning: there are sequence names (like 'NP117#hap#178') that do not match the Pangenome Sequence Naming (PanSN). [pggb] ERROR: -n/--n-haplotypes must be greater than or equal to 1 when the Pangenome Sequence Naming (PanSN) is not respected.

Unsure what the issue is as the fastix example is:

fastix -p "gen#1#" genome.fa > genome_prefixed.fa

Any insights would be greatly appreciated!

[AndreaGuarracino]

PanSN has become a bit stricter recently. The haplotype ID must be a number (0, 1, ...), no hap0, hap1, ...

…

________________________________ From: SquRunner ***@***.***> Sent: Wednesday, January 1, 2025 09:53 To: pangenome/pggb ***@***.***> Cc: Subscribed ***@***.***> Subject: [pangenome/pggb] PanSN naming issue in pggb fastas (Issue #437) I am having an issue with the PanSN naming for pggb fastas and would love any insight. In preparing for pggb, I am running: fastix -p "NP117#hap#" 117_Assembly.fasta > 117_shasta_fastix_output.fasta But run into naming issues with: pggb -i combined_aligned_contigs.fasta.gz -o pangenome [pggb] warning: there are sequence names (like 'NP117#hap#178') that do not match the Pangenome Sequence Naming (PanSN). [pggb] ERROR: -n/--n-haplotypes must be greater than or equal to 1 when the Pangenome Sequence Naming (PanSN) is not respected. Unsure what the issue is as the fastix example is: fastix -p "gen#1#" genome.fa > genome_prefixed.fa Any insights would be greatly appreciated! — Reply to this email directly, view it on GitHub<#437>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AO26XHUEZDWOXP3X6ZNWP3T2IQFPLAVCNFSM6AAAAABUOYCRTWVHI2DSMVQWIX3LMV43ASLTON2WKOZSG43DKMJTHAZTCNQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[SquRunner]

Ah! I see... Names like "NP117#1#101" worked. Thanks so much for the help!

…

________________________________ From: Andrea Guarracino ***@***.***> Sent: Wednesday, January 1, 2025 10:59 AM To: pangenome/pggb ***@***.***> Cc: Cara Love ***@***.***>; Author ***@***.***> Subject: Re: [pangenome/pggb] PanSN naming issue in pggb fastas (Issue #437) PanSN has become a bit stricter recently. The haplotype ID must be a number (0, 1, ...), no hap0, hap1, ...

________________________________ From: SquRunner ***@***.***> Sent: Wednesday, January 1, 2025 09:53 To: pangenome/pggb ***@***.***> Cc: Subscribed ***@***.***> Subject: [pangenome/pggb] PanSN naming issue in pggb fastas (Issue #437) I am having an issue with the PanSN naming for pggb fastas and would love any insight. In preparing for pggb, I am running: fastix -p "NP117#hap#" 117_Assembly.fasta > 117_shasta_fastix_output.fasta But run into naming issues with: pggb -i combined_aligned_contigs.fasta.gz -o pangenome [pggb] warning: there are sequence names (like 'NP117#hap#178') that do not match the Pangenome Sequence Naming (PanSN). [pggb] ERROR: -n/--n-haplotypes must be greater than or equal to 1 when the Pangenome Sequence Naming (PanSN) is not respected. Unsure what the issue is as the fastix example is: fastix -p "gen#1#" genome.fa > genome_prefixed.fa Any insights would be greatly appreciated! — Reply to this email directly, view it on GitHub<#437>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AO26XHUEZDWOXP3X6ZNWP3T2IQFPLAVCNFSM6AAAAABUOYCRTWVHI2DSMVQWIX3LMV43ASLTON2WKOZSG43DKMJTHAZTCNQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub<#437 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BBVXFJCOSMWG2PROSY7KZP32IQGETAVCNFSM6AAAAABUOYCRTWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNRXGA3DAMZQGU>. You are receiving this because you authored the thread.Message ID: ***@***.***>