关于step3的报错

[kikokhalifa]

您好，在使用Rscript /home/bin/singlecell.r -i /mnt/d/scTEST/config.ini 命令后，出现以下报错。
请问该如何解决呢
2023-12-17 10:11:41 INFO::savefig at /mnt/d/outfile/step3/umap/plotby_ident
2023-12-17 10:11:43 INFO::savefig at /mnt/d/outfile/step3/umap/plotall_ident
Error in geom_point():
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in FUN():
! object 'UMAP_1' not found
Backtrace:
▆

1. ├─global savepdf(...)
2. │ └─ggplot2::ggsave(...)
3. │ ├─grid::grid.draw(plot)
4. │ └─ggplot2:::grid.draw.ggplot(plot)
5. │ ├─base::print(x)
6. │ └─ggplot2:::print.ggplot(x)
7. │ ├─ggplot2::ggplot_build(x)
8. │ └─ggplot2:::ggplot_build.ggplot(x)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$compute_aesthetics(d, plot)
18. │ └─ggplot2 (local) compute_aesthetics(..., self = self)
19. │ └─ggplot2:::scales_add_defaults(...)
20. │ └─base::lapply(aesthetics[new_aesthetics], eval_tidy, data = data)
21. │ └─rlang (local) FUN(X[[i]], ...)
22. └─base::.handleSimpleError(...)
23. └─rlang (local) h(simpleError(msg, call))

24. └─handlers[[1L]](cnd)
    

25.   └─cli::cli_abort(...)
    

26.     └─rlang::abort(...)
    

Warning messages:
1: In dir.create(paste(outdir, "step3", sep = "/"), recursive = T) :
'/mnt/d/outfile/step3' already exists
2: In dir.create(paste(outdir, "step3", "pca", sep = "/")) :
'/mnt/d/outfile/step3/pca' already exists
3: In ElbowPlot(pbmcall, csc$step3$elbowdims) :
The object only has information for 50 reductions
4: In dir.create(paste(outdir, "step3", cscumap, sep = "/")) :
'/mnt/d/outfile/step3/umap' already exists
Execution halted

[zhangjing1123]

您好，这个问题还从没遇到过，麻烦提供一下config文件和对应的rds文件；可以传到方便下载的云盘，我们下载后运行排查

[kikokhalifa]

感谢您的回复 该报错是在wsl2上运行时出现的，目前我准备在ubuntu中重新运行一下。到时给您反馈谢谢 ***@***.***

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---- 回复的原邮件 ---- 发件人 ***@***.***> 发送日期 2023年12月18日 09:22 收件人 ***@***.***> 抄送人 ***@***.***> , ***@***.***> 主题 Re: [OpenGene/scrnapip] 关于step3的报错 (Issue #3) 你，这个问题还从没遇到过，需要提供一下config文件，最好再提供一下对应的rds文件；可以传到方便下载的云盘 —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>