Stacks 1.44 Error

Question

[virtualinterlect]

Hi,

I installed stacks using conda, and stacks 1.44 was installed. However, I would have loved to have the recent version 2.53 at least.

I decided to run denovo.pl on the version 1.44 and the error message I got was

Unknown command line option: '--popmap'

My command is

denovo_map.pl --samples /public/home/WHC_BBT/Substacks21/ \
              --popmap /public/home/WHC_BBT/Substacks21/popu-sub.txt \
              -o /public/home/WHC_BBT/Substacks21/M3/ \
              -M 3\
              -n 3 \
              -X "populations: -r 0.8 -T 10" \
              --paired

How can I overcome this?

Do I need to remove 1.44 and install 2.53 directly instead of using conda?

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

Answer 1

[h.mon]

Bioconda has a recipe for Stacks 2.53, it is unclear how you ended up with version 1.44.Install Stacks in a new conda environment:

conda create -n Stacks-2.53
conda activate Stacks-2.53
conda install Stacks=2.53  -c bioconda