Bryce Kille

Thanks for posting the issue, thats definitely not right... I'll take a look and see if I can replicate it. In the meantime, please feel free to post the stderr...

Ahh! Ok that makes sense. As far as the different results based on the reference goes, it looks MashMap is finding twice as many unique _k_-mer seeds in the uncompressed...

From looking at the output logs, the sketch size of the compressed version was 20, but the uncompressed was 40. I was replicate the issue and actually, it looks like...

As a side note, with `--noSplit`, the sketch size is the same for each query sequence, i.e. even a query contig thats 10Mbp will only have 40 sketched _k_-mers. If...

`mkl` was listed as an osx dependency in conda for v2.0, but I removed it for v3.0 and up since we don't link to it. Nevertheless, someone from our lab...

@Kadsae, It is not surprising that the results differ between the two Parsnp versions, as much has changed. Regarding the homoplastic vs unique, is this something that you believe to...

Hi @mlarjim So sorry for the late reply. I'll make sure the next update of Parsnp (which I'll release within the next week or so) will automatically check for this....

Great! Ok for the new issue where it seems to stall on ~9 genomes but works fine on ~300, are the genomes in the group of 9 roughly the same...

Hi @ingridvanw The command that fails is ``` harvesttools -q -o parsnp.ggr -f GCF_000014985.1_ASM1498v1_genomic.fna.ref -x parsnp.xmfa ``` I'm not sure how parsnp even ends up running that command, as there...

Hi @jodyphelan I've fixed the position issue you described above. I also added the VCF format spec to the first line of the VCF: ``` ##fileformat=VCFv4.2 ``` which fixed the...