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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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RunSCVELO Error in py_call_impl(callable, call_args$unnamed, call_args$named) #157

Open Githubxsw opened 11 months ago

Githubxsw commented 11 months ago

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 commented 11 months ago

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 commented 11 months ago

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

realzehuali commented 11 months ago

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 commented 9 months ago

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 commented 8 months ago

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.