RunSCVELO Error in py_call_impl(callable, call_args$unnamed, call_args$named)

[Githubxsw]

Normal_Epi <- RunSCVELO(srt = Normal_Epi , group_by = "Anno2", linear_reduction = "pca", nonlinear_reduction = "umap", mode = "stochastic", return_seurat = TRUE)
Assay 'integrated' is in the srt object but not converted.
'misc' slot is not converted.
'tools' slot is not converted.
Renamed 'umap' to convention 'X_umap' (adata.obsm).
'spliced' data must be provided.
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
SystemExit: None
Run reticulate::py_last_error() for details.

reticulate::py_last_error()
── Python Exception Message
Traceback (most recent call last):
File "/gpfs/share/home/2211110320/98Software/miniconda3/envs/R/envs/scpenv/lib/R/library/SCP/python/SCP_analysis.py", line 66, in SCVELO
exit()
File "/gpfs/share/home/2211110320/98Software/miniconda3/envs/R/envs/SCP_env/lib/python3.8/_sitebuiltins.py", line 26, in call
raise SystemExit(code)
SystemExit: None

── R Traceback
▆

1. └─SCP::RunSCVELO(...)
2. ├─base::do.call(SCP_analysis$SCVELO, args)
3. └─reticulate (local) <python.builtin.function>(...)

4. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
   

How I can solve this error. Thank you.

[ZhangHao]

The estimation of cell velocity requires the presence of "spliced" and "unspliced" assays in your Seurat object. These matrices can be generated using velocyto, bustools, or alevin

[realzehuali]

Same issue. Using data("pancreas_sub") also failed in the same way.

[realzehuali]

data("pancreas_sub")
pancreas_sub <- RunSCVELO(

• srt = pancreas_sub, group_by = "SubCellType",
• linear_reduction = "PCA", nonlinear_reduction = "UMAP"
• )
  'misc' slot is not converted.
  'tools' slot is not converted.
  Filtered out 12123 genes that are detected 30 counts (shared).
  Normalized count data: X, spliced, unspliced.
  Logarithmized X.
  computing neighbors
  finished (0:00:07) --> added
  'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
  computing moments based on connectivities
  finished (0:00:00) --> added
  'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
  computing velocities
  finished (0:00:00) --> added
  'stochastic', velocity vectors for each individual cell (adata.layers)
  computing velocity graph (using 1/16 cores)
  0%| | 0/1000 [00:00<?, ?cells/s]
  Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
  ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (1, 4) + inhomogeneous part.
  Run reticulate::py_last_error() for details.

[Georgewwek]

Hey, I hope this helps. The issue is not caused by the SCP package itself. You need to make sure that you have pandas==1.1.5 and numpy==1.21.1 installed.（py_install("pandas==1.1.5") and py_install("numpy==1.21.1")）

[Boyce Dare]

Hey, I hope this helps. The issue is not caused by the SCP package itself. You need to make sure that you have pandas==1.1.5 and numpy==1.21.1 installed.（py_install("pandas==1.1.5") and py_install("numpy==1.21.1")）

Thank you for your help. However, it did not work. I met the same issue with the "pancreas_sub" data.