Alex Leonard

I tried with `--trio-dual` and the results are quite similar with large regions still missing from one haplotype. I don't think it is straightfoward to follow the *dip.p_utg.gfa* gets split...

This a summary of reference-scaffolded chromosomes for some of the different modes discussed. The dual assemblies were taken from `.bp.hap1.p_ctg.gfa` etc. There is still some extreme variation even in the...

The total files are ~60 Gb so above the hosting limit I have. I've uploaded the [asm.ec.bin](https://polybox.ethz.ch/index.php/s/ub0tY7iFCZ9rVfH) for now, and once you confirm you have downloaded that I'll remove that...

I didn't extensively test how much of this could be trimmed further, but I found I can drop `abseil-cpp` (which is only available as an older version compared to `libabseil`)...

Normalising the vcf helped, but now running into a new error about a recursion limit. There were previously many errors about deletion paths not being correct. ``` dummy_node_adder 2021-12-08 16:26:15,292...

I use a modified version of this as our LSF config seems to be slightly different, but happy to help here where possible.

Sorry, lost track of this. Our HPC was supposedly transitioning to slurm as well for Sep 1, but hasn't happened yet. I was trying to find out more, but likely...

Is "pruning" still a supported step or is it not recommended anymore? This issue happens because the pruning step happening [here](https://github.com/ChaissonLab/danbing-tk/blob/c997e5875f79a5c8d486b900856b2225dbf3fc0c/pipeline/GoodPanGenomeGraph.snakefile#L319) is using the per-assembly graph which has not yet...

Started a draft in #19, hopefully will allow pruning in the new pipeline

Appears to successfully reach the end, and the resulting pruned pan files are similar enough to my tests with v1.0 without pruning to feel like the files at least are...