plubbe

Hi @rbouckaert - Thanks for responding. I haven't tried reliably reproducing the issue, but I for my part it was happening due to the taxon names being too long. I...

I have run PSMC on both Linux and Mac systems, locally and remotely, and have experienced no technological issues other than those related to the cryptic (non-existant) error messages and...

I've thought about this for a little while now. I have a feeling it is the -t flag which is causing the great difference in the graphs. I think the...

Typically this error is caused when there was a problem generating the file, either because the input is corrupted, or because it can't be found. Unfortunately the psmc command won't...

Hi @Giov12 ! I figured out this artifact was mostly due to the sequencing set-up I used; I had different insert sizes for one individual sample that I'd sequenced and...

Try checking the contents of each intermediate file- your input . bam and the .fq.gz output. I had the same problem which was solved when I realized I was pointing...

Depends on how taxonomically distant the reference is from your data. You may find [this paper helpful from Prasad et al, 2021](https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13457)

A general threshold is >18x coverage. I would also apply some filters to remove regions with