Rebecca S

lsort Index error

3

I ran the following command: svtools lsort P001_WD11-smoove.genotyped.vcf.gz P001_WD12-smoove.genotyped.vcf.gz P001_WE11-smoove.genotyped.vcf.gz | bgzip -c > sorted.vcf.gz And I get this error: Traceback (most recent call last): File "/home/ubuntu/progs/miniconda3/envs/smoove/bin/lsort", line 70, in...

I'm using pxbp version 1.3 and the command pxbp -t rs_test_rr.trees -o rs_test.txt. Trees are rooted. The output (full output attached) has OUTGROUP repeated multiple times in a clade. Additionally,...

calculating without gradient (might want to try a different optad=VALUE)

1

I have run TreePl by first running Prime and copying and pasting the generated values at the bottom of the configuration file: opt = 4 moredetail optad = 1 moredetailad...

I have a multiple, similar data sets. In a few of them, one or two chromosomes (different chromosomes in each data set) I get the following error: In rm(list =...