Error of dataset path parameter under Ubuntu18.04 when inferring trajectories #164
Description
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.
## 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!