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scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data
http://scvi-tools.org/
BSD 3-Clause "New" or "Revised" License
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AttributeError occurred when I use scVI method in R #2391

Closed redtorrentCN closed 8 months ago

redtorrentCN commented 8 months ago

Hi, all. I'm just a fresh man using scVI-tools in R env. when I try to integrate my data using scVI method, an error occurred as following:

my code:

library(Seurat)
options(Seurat.object.assay.version = "v5")
library(SeuratData)
obj <- LoadData("ifnb")
obj <- subset(obj, nFeature_RNA > 1000)
obj[["RNA"]] <- split(obj[["RNA"]], f = obj$stim)
obj <- NormalizeData(obj)
obj <- FindVariableFeatures(obj)
library(reticulate)
Sys.setenv(RETICULATE_PYTHON="C:\\Miniconda\\envs\\py311scvi\\python.exe")
sc <- import("scanpy", convert = FALSE)
scvi <- import("scvi", convert = FALSE)
new_obj<-obj
new_obj[["RNA"]] <- as(object = obj[["RNA"]], Class = "Assay")
top2000 <- head(VariableFeatures(new_obj), 2000)
new_obj <- new_obj[top2000]
andata_obj <- sceasy::convertFormat(new_obj, 
                                    from="seurat",
                                    to="anndata", 
                                    main_layer="counts",
                                    drop_single_values=FALSE)
scvi$model$SCVI$setup_anndata(andata_obj,batch_key = 'stim')
model = scvi$model$SCVI(andata_obj)
model$train()

Error

TPU available: False, using: 0 TPU cores
Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
  AttributeError: 'DataSplitter' object has no attribute '_has_setup_TrainerFn.FITTING'

── Python Exception Message ─────────────────────────────────────────────────────────────
Traceback (most recent call last):
  File "C:\Miniconda\envs\py311scvi\Lib\site-packages\scvi\model\base\_training_mixin.py", line 77, in train
    return runner()
           ^^^^^^^^
  File "C:\Miniconda\envs\py311scvi\Lib\site-packages\scvi\train\_trainrunner.py", line 72, in __call__
    self.trainer.fit(self.training_plan, self.data_splitter)
  File "C:\Miniconda\envs\py311scvi\Lib\site-packages\scvi\train\_trainer.py", line 177, in fit
    super().fit(*args, **kwargs)
  File "C:\Miniconda\envs\py311scvi\Lib\site-packages\pytorch_lightning\trainer\trainer.py", line 460, in fit
    self._run(model)
  File "C:\Miniconda\envs\py311scvi\Lib\site-packages\pytorch_lightning\trainer\trainer.py", line 715, in _run
    self.call_setup_hook(model)  # allow user to setup lightning_module in accelerator environment
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Miniconda\envs\py311scvi\Lib\site-packages\pytorch_lightning\trainer\trainer.py", line 1164, in call_setup_hook
    self.datamodule.setup(stage=fn)
  File "C:\Miniconda\envs\py311scvi\Lib\site-packages\pytorch_lightning\core\datamodule.py", line 376, in wrapped_fn
    has_run = getattr(obj, attr)
              ^^^^^^^^^^^^^^^^^^
AttributeError: 'DataSplitter' object has no attribute '_has_setup_TrainerFn.FITTING'

── R Traceback ──────────────────────────────────────────────────────────────────────────
    ▆
 1. └─model$train(max_epochs = as.integer(400))
 2.   └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)

conda list info:

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abseil-cpp                20230802.0           h5da7b33_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
absl-py                   2.0.0              pyhd8ed1ab_0    conda-forge
aiohttp                   3.9.1           py311ha68e1ae_0    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
anndata                   0.10.3             pyhd8ed1ab_0    conda-forge
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brotli                    1.1.0                hcfcfb64_1    conda-forge
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c-ares                    1.24.0               hcfcfb64_0    conda-forge
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cached-property           1.5.2                hd8ed1ab_1    conda-forge
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certifi                   2023.11.17         pyhd8ed1ab_0    conda-forge
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grpcio                    1.48.2          py311h6772dbd_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
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icu                       73.2                 h63175ca_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
igraph                    0.10.8               h0e101eb_0    conda-forge
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libhwloc                  2.9.3           default_haede6df_1009    conda-forge
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libsodium                 1.0.18               h8d14728_1    conda-forge
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r-colorspace              2.1_0             r41h6d2157b_1    conda-forge
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r-crayon                  1.5.2             r41hc72bb7e_1    conda-forge
r-crul                    1.4.0             r41h785f33e_0    conda-forge
r-curl                    4.3.3             r41h6d2157b_2    conda-forge
r-data.table              1.14.10           r41h6d2157b_0    conda-forge
r-dbi                     1.1.3             r41hc72bb7e_1    conda-forge
r-dbplyr                  2.3.2             r41hc72bb7e_0    conda-forge
r-diagram                 1.6.5             r41ha770c72_1    conda-forge
r-digest                  0.6.33            r41ha856d6a_0    conda-forge
r-dplyr                   1.1.4             r41ha856d6a_0    conda-forge
r-dtplyr                  1.3.1             r41hc72bb7e_0    conda-forge
r-e1071                   1.7_14            r41ha856d6a_0    conda-forge
r-ellipsis                0.3.2             r41h6d2157b_2    conda-forge
r-essentials              4.1             r41hd8ed1ab_2003    conda-forge
r-evaluate                0.21              r41hc72bb7e_0    conda-forge
r-fansi                   1.0.6             r41h6d2157b_0    conda-forge
r-farver                  2.1.1             r41ha856d6a_2    conda-forge
r-fastmap                 1.1.1             r41ha856d6a_1    conda-forge
r-fontawesome             0.5.1             r41hc72bb7e_0    conda-forge
r-forcats                 1.0.0             r41hc72bb7e_0    conda-forge
r-foreach                 1.5.2             r41hc72bb7e_1    conda-forge
r-foreign                 0.8_86            r41h6d2157b_0    conda-forge
r-formatr                 1.14              r41hc72bb7e_0    conda-forge
r-fs                      1.6.3             r41ha856d6a_0    conda-forge
r-future                  1.32.0            r41hc72bb7e_0    conda-forge
r-future.apply            1.11.0            r41hc72bb7e_0    conda-forge
r-gargle                  1.4.0             r41h785f33e_0    conda-forge
r-generics                0.1.3             r41hc72bb7e_1    conda-forge
r-ggplot2                 3.4.2             r41hc72bb7e_0    conda-forge
r-gistr                   0.9.0             r41hc72bb7e_1    conda-forge
r-glmnet                  4.1_2             r41he816bda_1    conda-forge
r-globals                 0.16.2            r41hc72bb7e_0    conda-forge
r-glue                    1.6.2             r41h6d2157b_2    conda-forge
r-googledrive             2.1.0             r41hc72bb7e_0    conda-forge
r-googlesheets4           1.1.0             r41h785f33e_0    conda-forge
r-gower                   1.0.1             r41h6d2157b_1    conda-forge
r-gtable                  0.3.3             r41hc72bb7e_0    conda-forge
r-hardhat                 1.3.0             r41hc72bb7e_0    conda-forge
r-haven                   2.5.4             r41ha856d6a_0    conda-forge
r-here                    1.0.1             r41hc72bb7e_1    conda-forge
r-hexbin                  1.28.3            r41he816bda_1    conda-forge
r-highr                   0.10              r41hc72bb7e_0    conda-forge
r-hms                     1.1.3             r41hc72bb7e_0    conda-forge
r-htmltools               0.5.7             r41ha856d6a_0    conda-forge
r-htmlwidgets             1.6.2             r41hc72bb7e_0    conda-forge
r-httpcode                0.3.0             r41h57928b3_3    conda-forge
r-httpuv                  1.6.13            r41ha856d6a_0    conda-forge
r-httr                    1.4.6             r41hc72bb7e_0    conda-forge
r-ids                     1.0.1             r41hc72bb7e_2    conda-forge
r-ipred                   0.9_14            r41h6d2157b_1    conda-forge
r-irdisplay               1.1               r41hd8ed1ab_1    conda-forge
r-irkernel                1.3.2             r41h785f33e_0    conda-forge
r-isoband                 0.2.7             r41ha856d6a_2    conda-forge
r-iterators               1.0.14            r41hc72bb7e_1    conda-forge
r-jquerylib               0.1.4             r41hc72bb7e_1    conda-forge
r-jsonlite                1.8.8             r41h6d2157b_0    conda-forge
r-kernsmooth              2.23_22           r41hd95e14d_0    conda-forge
r-knitr                   1.43              r41hc72bb7e_0    conda-forge
r-labeling                0.4.2             r41hc72bb7e_2    conda-forge
r-later                   1.3.2             r41ha856d6a_0    conda-forge
r-lattice                 0.22_5            r41h6d2157b_0    conda-forge
r-lava                    1.7.2.1           r41hc72bb7e_0    conda-forge
r-lazyeval                0.2.2             r41h6d2157b_4    conda-forge
r-lifecycle               1.0.3             r41hc72bb7e_1    conda-forge
r-listenv                 0.9.0             r41hc72bb7e_0    conda-forge
r-lobstr                  1.1.2             r41ha856d6a_3    conda-forge
r-lubridate               1.9.3             r41h6d2157b_0    conda-forge
r-magrittr                2.0.3             r41h6d2157b_2    conda-forge
r-maps                    3.4.2             r41h6d2157b_0    conda-forge
r-mass                    7.3_58.3          r41h6d2157b_0    conda-forge
r-matrix                  1.6_4             r41hb9981e2_0    conda-forge
r-memoise                 2.0.1             r41hc72bb7e_1    conda-forge
r-mgcv                    1.9_1             r41hb9981e2_0    conda-forge
r-mime                    0.12              r41h6d2157b_2    conda-forge
r-modelmetrics            1.2.2.2           r41ha856d6a_3    conda-forge
r-modelr                  0.1.11            r41hc72bb7e_0    conda-forge
r-munsell                 0.5.0           r41hc72bb7e_1005    conda-forge
r-nlme                    3.1_164           r41he816bda_0    conda-forge
r-nnet                    7.3_19            r41h6d2157b_1    conda-forge
r-numderiv                2016.8_1.1        r41hc72bb7e_4    conda-forge
r-openssl                 2.0.6             r41h81a3cea_1    conda-forge
r-parallelly              1.36.0            r41hc72bb7e_0    conda-forge
r-pbdzmq                  0.3_10            r41h05e23a2_1    conda-forge
r-pillar                  1.9.0             r41hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r41hc72bb7e_2    conda-forge
r-plyr                    1.8.9             r41ha856d6a_0    conda-forge
r-png                     0.1_8             r41h6d2157b_1    conda-forge
r-prettyunits             1.1.1             r41hc72bb7e_2    conda-forge
r-proc                    1.18.5            r41ha856d6a_0    conda-forge
r-processx                3.8.3             r41h6d2157b_0    conda-forge
r-prodlim                 2023.08.28        r41ha856d6a_0    conda-forge
r-progress                1.2.2             r41hc72bb7e_3    conda-forge
r-progressr               0.13.0            r41hc72bb7e_0    conda-forge
r-promises                1.2.1             r41ha856d6a_0    conda-forge
r-proxy                   0.4_27            r41h6d2157b_2    conda-forge
r-pryr                    0.1.6             r41ha856d6a_1    conda-forge
r-ps                      1.7.5             r41h6d2157b_1    conda-forge
r-purrr                   1.0.2             r41h6d2157b_0    conda-forge
r-quantmod                0.4.22            r41hc72bb7e_0    conda-forge
r-r6                      2.5.1             r41hc72bb7e_1    conda-forge
r-ragg                    1.2.5             r41hb5fc66f_0    conda-forge
r-randomforest            4.7_1.1           r41he816bda_2    conda-forge
r-rappdirs                0.3.3             r41h6d2157b_2    conda-forge
r-rbokeh                  0.5.2             r41hc72bb7e_2    conda-forge
r-rcolorbrewer            1.1_3             r41h785f33e_1    conda-forge
r-rcpp                    1.0.11            r41ha856d6a_0    conda-forge
r-rcpptoml                0.1.7             r41ha856d6a_2    conda-forge
r-readr                   2.1.4             r41ha856d6a_1    conda-forge
r-readxl                  1.4.3             r41h1c2d66b_0    conda-forge
r-recipes                 1.0.6             r41hc72bb7e_0    conda-forge
r-recommended             4.1             r41hd8ed1ab_1005    conda-forge
r-rematch                 1.0.1           r41hc72bb7e_1005    conda-forge
r-rematch2                2.1.2             r41hc72bb7e_2    conda-forge
r-repr                    1.1.6             r41h785f33e_0    conda-forge
r-reprex                  2.0.2             r41hc72bb7e_1    conda-forge
r-reshape2                1.4.4             r41ha856d6a_3    conda-forge
r-reticulate              1.34.0            r41ha856d6a_0    conda-forge
r-rlang                   1.1.2             r41ha856d6a_0    conda-forge
r-rmarkdown               2.22              r41hc72bb7e_0    conda-forge
r-rpart                   4.1.23            r41h6d2157b_0    conda-forge
r-rprojroot               2.0.3             r41hc72bb7e_1    conda-forge
r-rstudioapi              0.14              r41hc72bb7e_1    conda-forge
r-rvest                   1.0.3             r41hc72bb7e_1    conda-forge
r-sass                    0.4.8             r41ha856d6a_0    conda-forge
r-scales                  1.2.1             r41hc72bb7e_1    conda-forge
r-selectr                 0.4_2             r41hc72bb7e_2    conda-forge
r-shape                   1.4.6             r41ha770c72_1    conda-forge
r-shiny                   1.7.4             r41h785f33e_0    conda-forge
r-sourcetools             0.1.7_1           r41ha856d6a_1    conda-forge
r-spatial                 7.3_17            r41h6d2157b_0    conda-forge
r-squarem                 2021.1            r41hc72bb7e_1    conda-forge
r-stringi                 1.8.3             r41ha856d6a_0    conda-forge
r-stringr                 1.5.0             r41h785f33e_0    conda-forge
r-survival                3.5_7             r41h6d2157b_0    conda-forge
r-sys                     3.4.2             r41h6d2157b_1    conda-forge
r-systemfonts             1.0.5             r41h93c4b31_0    conda-forge
r-textshaping             0.3.6             r41haa3e5ab_1    conda-forge
r-tibble                  3.2.1             r41h6d2157b_2    conda-forge
r-tidyr                   1.3.0             r41ha856d6a_1    conda-forge
r-tidyselect              1.2.0             r41h6addd8b_1    conda-forge
r-tidyverse               2.0.0             r41h785f33e_0    conda-forge
r-timechange              0.2.0             r41ha856d6a_1    conda-forge
r-timedate                4022.108          r41hc72bb7e_0    conda-forge
r-tinytex                 0.45              r41hc72bb7e_0    conda-forge
r-triebeard               0.4.1             r41ha856d6a_1    conda-forge
r-ttr                     0.24.4            r41h6d2157b_0    conda-forge
r-tzdb                    0.4.0             r41ha856d6a_1    conda-forge
r-urltools                1.7.3             r41ha856d6a_4    conda-forge
r-utf8                    1.2.4             r41h6d2157b_0    conda-forge
r-uuid                    1.1_1             r41h6d2157b_0    conda-forge
r-vctrs                   0.6.5             r41ha856d6a_0    conda-forge
r-viridislite             0.4.1             r41hc72bb7e_1    conda-forge
r-vroom                   1.6.5             r41ha856d6a_0    conda-forge
r-withr                   2.5.0             r41hc72bb7e_1    conda-forge
r-xfun                    0.41              r41ha856d6a_0    conda-forge
r-xml2                    1.3.3             r41ha856d6a_2    conda-forge
r-xtable                  1.8_4             r41hc72bb7e_4    conda-forge
r-xts                     0.13.1            r41h6d2157b_1    conda-forge
r-yaml                    2.3.8             r41h6d2157b_0    conda-forge
r-zoo                     1.8_12            r41h6d2157b_1    conda-forge
re2                       2022.04.01           h0e60522_0    conda-forge
referencing               0.32.0             pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      13.7.0             pyhd8ed1ab_0    conda-forge
rpds-py                   0.16.2          py311hc37eb10_0    conda-forge
rsa                       4.9                pyhd8ed1ab_0    conda-forge
scanpy                    1.9.6              pyhd8ed1ab_1    conda-forge
scikit-learn              1.3.2           py311h142b183_2    conda-forge
scipy                     1.11.4          py311h0b4df5a_0    conda-forge
scvi-tools                0.14.6             pyhd8ed1ab_0    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
send2trash                1.8.2              pyh08f2357_0    conda-forge
session-info              1.0.0              pyhd8ed1ab_0    conda-forge
setuptools                57.4.0          py311h1ea47a8_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sqlite                    3.41.2               h2bbff1b_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.14.1          py311h59ca53f_0    conda-forge
stdlib-list               0.8.0              pyhd8ed1ab_0    conda-forge
sympy                     1.12               pyh04b8f61_3    conda-forge
tbb                       2021.11.0            h91493d7_0    conda-forge
tensorboard               2.15.1             pyhd8ed1ab_0    conda-forge
tensorboard-data-server   0.7.0           py311h1ea47a8_1    conda-forge
terminado                 0.18.0             pyh5737063_0    conda-forge
texttable                 1.7.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.2.0              pyha21a80b_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h2bbff1b_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
torchmetrics              0.7.0                    pypi_0    pypi
tornado                   6.3.3           py311ha68e1ae_1    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.1             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.8.19.14          pyhd8ed1ab_0    conda-forge
typing-extensions         4.9.0                hd8ed1ab_0    conda-forge
typing_extensions         4.9.0              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023c                h04d1e81_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
umap-learn                0.5.5           py311h1ea47a8_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.1.0              pyhd8ed1ab_0    conda-forge
vc                        14.2                 h21ff451_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
vc14_runtime              14.38.33130         h82b7239_18    conda-forge
vs2015_runtime            14.38.33130         hcb4865c_18    conda-forge
wcwidth                   0.2.12             pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.7.0              pyhd8ed1ab_0    conda-forge
werkzeug                  3.0.1              pyhd8ed1ab_0    conda-forge
wheel                     0.41.2          py311haa95532_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
widgetsnbextension        4.0.9              pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0              pyhd8ed1ab_6    conda-forge
winpty                    0.4.3                         4    conda-forge
xorg-libxau               1.0.11               hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.4.5                h8cc25b3_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
yaml                      0.2.5                h8ffe710_2    conda-forge
yarl                      1.9.3           py311ha68e1ae_0    conda-forge
zeromq                    4.3.5                h63175ca_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hcfcfb64_5    conda-forge
zstd                      1.5.5                hd43e919_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main

R version info:


Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] sceasy_0.0.7 reticulate_1.34.0 stxBrain.SeuratData_0.1.1 [4] pbmcsca.SeuratData_3.0.0 ifnb.SeuratData_3.1.0 SeuratData_0.2.2.9001
[7] Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-2 


above. it's a bit long text. thanks for your attention and answers. have a good day!
martinkim0 commented 8 months ago

Hi, it's likely that you will need to update PyTorch Lightning. You can do so with pip install -U lightning

redtorrentCN commented 8 months ago

Hi, it's likely that you will need to update PyTorch Lightning. You can do so with pip install -U lightning

Thank you ,sir. I'll try it.