isaacovercast
commented
3 years ago Branching and removing samples should work fine, and what you are doing looks good. The error is cropping up during _link_populations, which reads the pop_assign_file. Try removing the pop_assign_file and re-running the branch command, I bet it'll work fine.
carlahurt
Hello, I'm working on a denovo assembly of a large GBS dataset (~250 individuals, BIIIGGG salamander genome). I managed my way through step 6 and it took a while. Now I realize that I need to remove a couple of individuals that shouldn't be there. I'm hoping I can do this using branching without having to start over. I used the following code
ipyrad -p params-barb1.txt -b barb2 - B32, R1_E013Y2a, S7_E002Y2a, S7E16, S7E7, W1E12, W3E6, W3E7, B24, B26, BF1, BF2, D3_L019Y1, JS5, R7_L017Y1
and the log file is encountering and error:
loading Assembly: barbari1 from saved path: ~/miniconda3/barb_ipyrad/barbari1.json Traceback (most recent call last): File "/home/tntech.edu/churt/miniconda3/bin/ipyrad", line 10, in
sys.exit(main())
File "/home/tntech.edu/churt/miniconda3/lib/python3.8/site-packages/ipyrad/main.py", line 605, in main
CLI()
File "/home/tntech.edu/churt/miniconda3/lib/python3.8/site-packages/ipyrad/main.py", line 69, in init
self.get_assembly()
File "/home/tntech.edu/churt/miniconda3/lib/python3.8/site-packages/ipyrad/main.py", line 368, in get_assembly
data.set_params(key, param)
File "/home/tntech.edu/churt/miniconda3/lib/python3.8/site-packages/ipyrad/core/assembly.py", line 493, in set_params
setattr(self.params, param, newvalue)
File "/home/tntech.edu/churt/miniconda3/lib/python3.8/site-packages/ipyrad/core/params.py", line 267, in setattr
super().setattr(key, val)
File "/home/tntech.edu/churt/miniconda3/lib/python3.8/site-packages/ipyrad/core/params.py", line 721, in pop_assign_file
self._data._link_populations()
File "/home/tntech.edu/churt/miniconda3/lib/python3.8/site-packages/ipyrad/core/assembly.py", line 438, in _link_populations
if not all([popmax[i] >= popmins[i] for i in popdict]):
File "/home/tntech.edu/churt/miniconda3/lib/python3.8/site-packages/ipyrad/core/assembly.py", line 438, in
if not all([popmax[i] >= popmins[i] for i in popdict]):
KeyError: '1'
Is it possible to remove individuals at this stage? Please advise.
I'm attaching my params file for reference: params-barb1.txt