John Lees comments

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                                            John Lees

hhalignment: did not find [x] match states in sequence [i]

Also to note, this does work on other input sequences

hhalignment: did not find [x] match states in sequence [i]

Thanks for the reply and trying to reproduce. Unfortunately little more info from my end > Do you have the full command line call that was passed to HHblits? >...

hhalignment: did not find [x] match states in sequence [i]

Thanks for looking into this further, and glad it ended up being reproducible. I guess for me the easiest solution will be to update the uniclust DB?

Turn exception handling off in nextclade_wasm/nextalign

Ah that's great – mostly just wanted to check this was on your radar as I didn't find this clear when I first used emscripten. I'd looked at one of...

Possibility of having a single header to include

Thanks for the quick reply! We've got our build working again without too much trouble, but this would be useful if it fits into your plans. For reference, this is...

bcftools csq cannot parse bacterial gff3 files

Ah I see, thanks a lot. Such a perl script would certainly be useful, but I'd guess it'd be difficult to cover all the variants of GFF files. I will...

Improve distance estimation

Comparing equation 3 in the paper to the current Monte Carlo method and/or using this method for drawing the tree?

Meta: Refactor code base

I became increasingly aware with the latest changes that a lot of parts of the code now are not as we would write them if doing this with our current...

Help with issues running poppunk in HPC environment

This is always a tricky one. Potentially we've got a memory related bug, these sometimes cause a crash and sometimes don't. First, it would be helpful to get a minimal...

Help with issues running poppunk in HPC environment

Ok that's useful. Would it be possible to share those two files? If not, I'll see if I can reproduce in a debugger with two test files of my own.