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-njmu]

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")）

[yfkaajrizt92]

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.