pangraph build crash

[mjohnpayne]

Hi Marco,

I am having pangraph crash on a particular input file (renamed to .txt and attached) with the following command:

pangraph-aarch64-apple-darwin build -s 20 -a 0.0 -b 6.666 -l 90 -j 10 sistr_filtered_input.fasta > sistr.json

[sistr_filtered_input.txt](https://github.com/user-attachments/files/23176347/sistr_filtered_input.txt

I get the following errors:

[31mThe application panicked (crashed). [0m
Message: [91;1massertion left == right failed
left: 1494
right: 1491 [0m
Location: [32mpackages/pangraph/src/align/nextclade/analyze/nuc_changes.rs [0m: [33m19 [0m
If you think it's a bug, consider reporting at: 'https://github.com/neherlab/pangraph/issues'
Backtrace omitted. Run with RUST_BACKTRACE=1 environment variable to display it.
Run with RUST_BACKTRACE=full to include source snippets.

Let me know if you need any more info (I tried setting RUST_BACKTRACE=full but it didn't change the amount of output). This is running on an M4 mac.

Cheers,
Michael

[mmolari]

Hi Michael,

thank you for providing the data, this makes debugging a lot easier!
In this case I believe that the bug is caused by the fact that four of the sequences have gaps, namely:

>Salmonella~fljB_SRR1272485|l,z13
>Salmonella~fljB_SRR1188448|l,z13
>Salmonella~fljB_SRR1918953|e,n,z15
>Salmonella~wzx_SRR5160124|V

Since pangraph expects un-aligned sequences without gaps, this creates a mismatch between the input sequence length and the output sequence length. If I remove these gap characters and re-run pangraph it seems to complete without issues.

I realize that the error message is not very helpful in this case, it might be wise to add a more informative message. Thank you for pointing it out!

Hope this solves it!

Cheers,
Marco

[mjohnpayne]

Great, thanks Marco. Probably should have found that myself but glad it is an easy fix!

Cheers,
Michael