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dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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Error during trajectory inference #109

Open SebRW opened 3 years ago

SebRW commented 3 years ago

I'm new to dynverse and I am trying to run my first trajectory analysis. I created my dataset from a seurat object as followed: 

dataset <- wrap_expression(
  expression = t(data.frame(seu@assays[["RNA"]]@data))
  counts = t(data.frame(seu@assays[["RNA"]]@counts))
)

Then added some info: 

dataset <- add_prior_information(
  dataset = dataset,
  start_id = naive_id, # a chr vector of my starting cells barcodes
  groups_id = groups_id, # a dataframe of my assigned seurat clusters
  dimred = seu@reductions[["umap"]]@cell.embeddings)

I followed the guidelines and selected "paga" for method

model <- infer_trajectory(dataset, method = "paga", verbose = TRUE)

At the end of the process I obtained the following: [...] INFO: Creating SIF file... /usr/local/lib/python3.7/site-packages/umap/rp_tree.py:450: NumbaWarning: Compilation is falling back to objec Error: Error during trajectory inference, see output above

What could possibly went wrong?

R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 19.3 Singularity is at correct version (>=3.0): 3.7.4 is installed Singularity test successful

KforKuma commented 3 years ago

I met the same problem with docker... The head is like: /usr/local/lib/python3.7/site-packages/umap/rp_tree.py:450: NumbaWarning: Compilation is falling back to object mode WITH looplifting enabled because Function "make_euclidean_tree" failed type inference due to: Cannot unify RandomProjectionTreeNode(array(int64, 1d, C), bool, none, none, none, none) and RandomProjectionTreeNode(none, bool, array(float32, 1d, C), float64, RandomProjectionTreeNode(array(int64, 1d, C), bool, none, none, none, none), RandomProjectionTreeNode(array(int64, 1d, C), bool, none, none, none, none)) for '$14.16', defined at /usr/local/lib/python3.7/site-packages/umap/rp_tree.py (457)