Closed ChadFibke closed 2 years ago
I think we have changed this so that it should work automatically from your lineage model, and produce output at all ranks. Can you try again, but just removing those two arguments?
I see the documentation is probably wrong on this, if this works we'll correct the instructions
Hi,
I removed the --rank and --assign-lineages, and it looks like PopPUNK is picking up the expected lineage cluster model. The program successfully ran!
PopPUNK: assign
(with backend: sketchlib v1.7.4
sketchlib: /home/chad.fibke/.conda/envs/POPpunk/lib/python3.9/site-packages/pp_sketchlib.cpython-39-x86_64-linux-gnu.so)
Graph-tools OpenMP parallelisation enabled: with 8 threads
Mode: Assigning clusters of query sequences
Loading lineage cluster model
Completed model loading
The rest of the output was related to qc and progress :). Thank you for the quick response!
Best, Chad
Ok excellent, I'll raise another issue to remind me to fix the docs for this case
Hi @johnlees, I hit another small snag described below:
Versions:
I wanted to use my previously constructed database (with strand-preserved and phased-codon options) to predict lineages of new samples. The database information is below:
I constructed a fitted model using the lineage option (due to poor population structure). I then used the following command to assign lineages to my query samples and got the following error:
I also could not see the --assign-lineages and --rank arguments when running
poppunk_assign --help
Any help would be appreciated :)
Best, Chad