Pavel V. Dimens

Would there be merit to me posting this there as well?

I can confirm this problem persists in the conda installation. Here is the `tree` of the working directory: ``` ├── asm_contigs_k49_a9_lr30x_b500_s2_sim0.85 │   ├── backbone.01.init.gfa │   ├── backbone.01.init.stat │   ├── backbone.02.weakEdge.gfa...

+1 to experiencing this on Manjaro + KDE

I'm using stock Plasma panel

I tested this on my real-world linkage map data and the method suggested by @cbird808 removes all of my contigs: ```bash > minCOV=$(echo $(($(wc -l namelist | cut -d" "...

Story of my life. My data is janky b/c we had to whole-genome-amplify all the samples prior to using ddRAD and there's a noticeable amount of bias from PCR and...

To follow up on this, the filtering should be an opt-in or opt-out to avoid situations like above.

That seems like a safe compromise.

@cbird808 Is this still an issue? If so, does this suggested fix continue to solve it? Does `--env _` need to be added to every instance of `parallel` ?

We're experimenting with an alternative way of generating the `mapped.bed`, and if this was to be implemented, I think a parsimonious way to implement it would be to generate the...