Open duohongrui opened 2 years ago
Hi, Dynverse is a powerful tool to infer and evaluate trajectories for single-cell RNA sequencing data. Several days ago, I met a tough problem under Ubuntu18.04 when inferring trajectories. The version of ti_slingshot is 1.0.3. The codes are below:
# Generate a reference data set.seed(1) a <- matrix(rpois(n = 2500, lambda = 2), nrow = 50) rownames(a) <- paste0("cell_", 1:ncol(a)) colnames(a) <- paste0("gene_", 1:nrow(a)) dataset_ref <- dynwrap::wrap_expression( counts = a, expression = log2(a+1) ) # Trajectory inference model_ref <- dynwrap::infer_trajectory(dataset_ref, 'slingshot', verbose = T)
The error said:
Error: Error: --dataset should contain a pathname of a .loom or .h5 file. Add a '-h' flag for help. Execution halted
However, the dataset path parameter is actually in the recording infomation.
Executing 'slingshot' on '20220404_163254__data_wrapper__pGINzXb8wh' With parameters: list(cluster_method = "pam", ndim = 20L, shrink = 1L, reweight = TRUE, reassign = TRUE, thresh = 0.001, maxit = 10L, stretch = 2L, smoother = "smooth.spline", shrink.method = "cosine") inputs: expression priors : Input saved to /tmp/RtmpuWLzCH/file31c92a48d72a/ti Running method using babelwhale Running /usr/bin/docker run --name 20220404_202410__container__FqdSy8fabq -e 'TMPDIR=/tmp2' --workdir /ti/workspace \ -v '/tmp/RtmpuWLzCH/file31c92a48d72a/ti:/ti' -v '/tmp/RtmpuWLzCH/file31c974a77030/tmp:/tmp2' \ 'dynverse/ti_slingshot:v1.0.3' --dataset /ti/input.h5 --output /ti/output.h5
Then, I tried these codes on Windows10 and everything is OK:
Executing 'slingshot' on '20220404_201956__data_wrapper__pGINzXb8wh' With parameters: list(cluster_method = "pam", ndim = 20L, shrink = 1L, reweight = TRUE, reassign = TRUE, thresh = 0.001, maxit = 10L, stretch = 2L, smoother = "smooth.spline", shrink.method = "cosine") inputs: expression priors : Input saved to C:\Users\duoho\AppData\Local\Temp\RtmpE9y0LN\fileb1453c66742/ti Running method using babelwhale Running "C:\PROGRA~1\Docker\Docker\RESOUR~1\bin\docker.exe" run --name \ 20220404_202301__container__Rw9GHleUH5 -e "TMPDIR=/tmp2" --workdir /ti/workspace -v \ "/c/Users/duoho/AppData/Local/Temp/RtmpE9y0LN/fileb1453c66742/ti:/ti" -v \ "/c/Users/duoho/AppData/Local/Temp/RtmpE9y0LN/fileb147ed6081/tmp:/tmp2" "dynverse/ti_slingshot:v1.0.3" \ --dataset /ti/input.h5 --output /ti/output.h5 Warning messages: 1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display 2: 'rgl_init' failed, running with rgl.useNULL = TRUE Using diagonal covariance matrix There were 50 or more warnings (use warnings() to see the first 50) Output saved to C:\Users\duoho\AppData\Local\Temp\RtmpE9y0LN\fileb1453c66742/ti/output.h5 Attempting to read in output with hdf5
The R environment under Ubuntu is below:
R version 4.0.0 (2020-04-24) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS Matrix products: default BLAS: /usr/local/lib/R/lib/libRblas.so LAPACK: /usr/local/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] amap_0.8-18 loaded via a namespace (and not attached): [1] babelwhale_1.0.3 plyr_1.8.7 igraph_1.3.0 lazyeval_0.2.2 [5] proxyC_0.2.4 splines_4.0.0 dynwrap_1.2.2 listenv_0.8.0 [9] scattermore_0.8 usethis_2.1.5 GenomeInfoDb_1.26.7 ggplot2_3.3.5 [13] digest_0.6.29 htmltools_0.5.2 fansi_1.0.3 memoise_2.0.1 [17] magrittr_2.0.3 dynfeature_1.0.0 carrier_0.1.0 tensor_1.5 [21] cluster_2.1.3 ROCR_1.0-11 tzdb_0.3.0 remotes_2.4.2 [25] globals_0.14.0 readr_2.1.2 RcppParallel_5.1.5 matrixStats_0.61.0 [29] dynutils_1.0.9 spatstat.sparse_2.1-0 prettyunits_1.1.1 colorspace_2.0-3 [33] ggrepel_0.9.1 dplyr_1.0.8 callr_3.7.0 crayon_1.5.1 [37] RCurl_1.98-1.6 jsonlite_1.8.0 spatstat.data_2.1-4 survival_3.3-1 [41] zoo_1.8-9 ape_5.6-2 glue_1.6.2 polyclip_1.10-0 [45] gtable_0.3.0 zlibbioc_1.36.0 XVector_0.30.0 leiden_0.3.9 [49] DelayedArray_0.16.3 pkgbuild_1.3.1 future.apply_1.8.1 SingleCellExperiment_1.12.0 [53] BiocGenerics_0.36.1 dynparam_1.0.0 abind_1.4-5 scales_1.1.1 [57] spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.8.3 viridisLite_0.4.0 [61] xtable_1.8-4 ctc_1.64.0 reticulate_1.24 spatstat.core_2.4-2 [65] stats4_4.0.0 htmlwidgets_1.5.4 httr_1.4.2 RColorBrewer_1.1-2 [69] ellipsis_0.3.2 Seurat_4.1.0 ica_1.0-2 pkgconfig_2.0.3 [73] uwot_0.1.11 deldir_1.0-6 utf8_1.2.2 tidyselect_1.1.2 [77] rlang_1.0.2 reshape2_1.4.4 later_1.3.0 cachem_1.0.6 [81] munsell_0.5.0 tools_4.0.0 cli_3.2.0 generics_0.1.2 [85] ranger_0.13.1 devtools_2.4.3 ggridges_0.5.3 stringr_1.4.0 [89] fastmap_1.1.0 yaml_2.3.5 goftest_1.2-3 fs_1.5.2 [93] processx_3.5.3 fitdistrplus_1.1-8 dyneval_0.9.9 purrr_0.3.4 [97] RANN_2.6.1 pbapply_1.5-0 future_1.24.0 nlme_3.1-157 [101] mime_0.12 rstudioapi_0.13 brio_1.1.3 compiler_4.0.0 [105] curl_4.3.2 plotly_4.10.0 png_0.1-7 testthat_3.1.3 [109] spatstat.utils_2.3-0 tibble_3.1.6 stringi_1.7.6 ps_1.6.0 [113] desc_1.4.1 lattice_0.20-45 Matrix_1.4-1 dynmethods_1.0.5 [117] vctrs_0.4.0 pillar_1.7.0 lifecycle_1.0.1 spatstat.geom_2.4-0 [121] lmtest_0.9-40 RcppAnnoy_0.0.19 data.table_1.14.2 cowplot_1.1.1 [125] bitops_1.0-7 irlba_2.3.5 httpuv_1.6.5 patchwork_1.1.1 [129] GenomicRanges_1.42.0 R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20 [133] gridExtra_2.3 IRanges_2.24.1 parallelly_1.30.0 sessioninfo_1.2.2 [137] codetools_0.2-18 MASS_7.3-56 assertthat_0.2.1 pkgload_1.2.4 [141] SummarizedExperiment_1.20.0 rprojroot_2.0.2 withr_2.5.0 SeuratObject_4.0.4 [145] sctransform_0.3.3 harmony_0.1.0 S4Vectors_0.28.1 GenomeInfoDbData_1.2.4 [149] mgcv_1.8-40 parallel_4.0.0 hms_1.1.1 grid_4.0.0 [153] rpart_4.1.16 tidyr_1.2.0 MatrixGenerics_1.2.1 Rtsne_0.15 [157] Biobase_2.50.0 shiny_1.7.1
I guess that this error is generated by fix_windows_path() function in the original codes because the change of path may not be valid under Linux OS.
fix_windows_path()
## https://github.com/dynverse/dynwrap/blob/master/R/method_create_ti_method_container.R output <- babelwhale::run( container_id = method$run$container_id, command = NULL, args = args, volumes = paste0(preproc_meta$dir_dynwrap %>% fix_windows_path(), ":/ti"), workspace = "/ti/workspace", verbose = preproc_meta$verbose, debug = preproc_meta$debug )
Could you please find out the reason and solve this problem? Thanks very much!
Hi, Dynverse is a powerful tool to infer and evaluate trajectories for single-cell RNA sequencing data. Several days ago, I met a tough problem under Ubuntu18.04 when inferring trajectories. The version of ti_slingshot is 1.0.3. The codes are below:
The error said:
However, the dataset path parameter is actually in the recording infomation.
Then, I tried these codes on Windows10 and everything is OK:
The R environment under Ubuntu is below:
I guess that this error is generated by
fix_windows_path()function in the original codes because the change of path may not be valid under Linux OS.Could you please find out the reason and solve this problem? Thanks very much!