Error in "model <- infer_trajectory(dataset, methods_selected, verbose = TRUE)"

Hi,

I have a problem to run the code

model <- infer_trajectory(dataset, methods_selected, verbose = TRUE)

In June I tried your package with some single cell data and followed your tutorial for that and it worked totally fine. A few days ago I tried to run exactly the same code with the same dataset, but it is not working anymore. So as there was an update for docker, I tried to set it back to the version I used before, but that didn't help. I run the following code:

library(Seurat)
library(dyno)
library(Matrix)
library(dplyr)

seu.data <- Read10X(data.dir = path)
seu<-CreateSeuratObject(seu.data, min.cells = 2,min.features = 200)
seuNorm <- NormalizeData(object = seu, normalization.method = "LogNormalize", scale.factor = 10000)

dataset <-wrap_expression(id         = "MyData",
                          expression = t(seuNorm@assays[[1]]@data),
                          counts     = t(seuNorm@assays[[1]]@counts) )

guidelines <- guidelines_shiny(dataset)
methods_selected <- guidelines$methods_selected[1] 

dataset <- add_prior_information(
  dataset,
  start_id = "AAACCTGAGAGGTTAT" 
)

model <- infer_trajectory(dataset, methods_selected,  verbose = TRUE)

I chose the method PAGA for a quick test, but R computes for hours. The output during that time is:

v0.9.9.04: Pulling from dynverse/ti_paga_tree
ab1fc7e4bf91: Pulling fs layer
66575050199c: Pulling fs layer
4d6ccd149fc3: Pulling fs layer
d588c72fe3f7: Pulling fs layer
c4efdd5f451e: Pulling fs layer
834a41c4efa6: Pulling fs layer
82fa28fdbeb3: Pulling fs layer
d9dcdde68429: Pulling fs layer
0512db24e6b5: Pulling fs layer
b8a1c4f7f22e: Pulling fs layer
035dd037a0ee: Pulling fs layer
fea30c11d7f1: Pulling fs layer
4fe9981d22c9: Pulling fs layer
696bc3423178: Pulling fs layer
0a65a0f5dcd1: Pulling fs layer
d0bb45d42c8e: Pulling fs layer
1a9616399b58: Pulling fs layer
32cd32510543: Pulling fs layer
6508acd2eecd: Pulling fs layer
479ce1a1b674: Pulling fs layer
6b6f799b42df: Pulling fs layer
868e7e7207d7: Pulling fs layer
aa9bdfcbcdf9: Pulling fs layer
fea30c11d7f1: Waiting
4fe9981d22c9: Waiting
696bc3423178: Waiting
0a65a0f5dcd1: Waiting
d0bb45d42c8e: Waiting
1a9616399b58: Waiting
32cd32510543: Waiting
6508acd2eecd: Waiting
479ce1a1b674: Waiting
6b6f799b42df: Waiting
868e7e7207d7: Waiting
aa9bdfcbcdf9: Waiting
82fa28fdbeb3: Waiting
d588c72fe3f7: Waiting
c4efdd5f451e: Waiting
834a41c4efa6: Waiting
d9dcdde68429: Waiting
0512db24e6b5: Waiting
b8a1c4f7f22e: Waiting
035dd037a0ee: Waiting
ab1fc7e4bf91: Verifying Checksum
ab1fc7e4bf91: Download complete
d588c72fe3f7: Verifying Checksum
d588c72fe3f7: Download complete
c4efdd5f451e: Verifying Checksum
c4efdd5f451e: Download complete
ab1fc7e4bf91: Pull complete
834a41c4efa6: Download complete
82fa28fdbeb3: Verifying Checksum
82fa28fdbeb3: Download complete
4d6ccd149fc3: Verifying Checksum
4d6ccd149fc3: Download complete
0512db24e6b5: Download complete
b8a1c4f7f22e: Verifying Checksum
b8a1c4f7f22e: Download complete
66575050199c: Verifying Checksum
66575050199c: Download complete
fea30c11d7f1: Verifying Checksum
fea30c11d7f1: Download complete
4fe9981d22c9: Verifying Checksum
4fe9981d22c9: Download complete
696bc3423178: Verifying Checksum
696bc3423178: Download complete
0a65a0f5dcd1: Download complete
66575050199c: Pull complete
035dd037a0ee: Verifying Checksum
035dd037a0ee: Download complete
d9dcdde68429: Verifying Checksum
d9dcdde68429: Download complete
1a9616399b58: Verifying Checksum
1a9616399b58: Download complete
d0bb45d42c8e: Verifying Checksum
d0bb45d42c8e: Download complete
32cd32510543: Verifying Checksum
32cd32510543: Download complete
6508acd2eecd: Verifying Checksum
6508acd2eecd: Download complete
6b6f799b42df: Verifying Checksum
6b6f799b42df: Download complete
4d6ccd149fc3: Pull complete
d588c72fe3f7: Pull complete
868e7e7207d7: Verifying Checksum
868e7e7207d7: Download complete
c4efdd5f451e: Pull complete
aa9bdfcbcdf9: Verifying Checksum
aa9bdfcbcdf9: Download complete
834a41c4efa6: Pull complete
82fa28fdbeb3: Pull complete
479ce1a1b674: Verifying Checksum
479ce1a1b674: Download complete
d9dcdde68429: Pull complete
0512db24e6b5: Pull complete
b8a1c4f7f22e: Pull complete
035dd037a0ee: Pull complete
fea30c11d7f1: Pull complete
4fe9981d22c9: Pull complete
696bc3423178: Pull complete
0a65a0f5dcd1: Pull complete
d0bb45d42c8e: Pull complete
1a9616399b58: Pull complete
32cd32510543: Pull complete
6508acd2eecd: Pull complete
479ce1a1b674: Pull complete
6b6f799b42df: Pull complete
868e7e7207d7: Pull complete
aa9bdfcbcdf9: Pull complete
Digest: sha256:18b8a4745e2f1d1e655a021f5949441b46dcaf32d8edbcb149650b5137ebc250
Status: Downloaded newer image for dynverse/ti_paga_tree:v0.9.9.04
Executing 'paga_tree' on 'MyData'
With parameters: list(n_neighbors = 15L, n_comps = 50L, n_dcs = 15L, resolution = 1L,     embedding_type = "fa"),
inputs: counts, and
priors : start_id
Loading required namespace: hdf5r
Input saved to D:\Users\sandra.wiedenmann\AppData\Local\Temp\Rtmp6hdAbw\file3f782c6a2b54/ti
Running method using babelwhale
Running "C:\PROGRA~1\Docker\Docker\RESOUR~1\bin\docker.exe" run --name 20190812_125834__container__jby8fcpVMu -e \
  "TMPDIR=/tmp2" --workdir /ti/workspace -v \
  "/d/Users/sandra.wiedenmann/AppData/Local/Temp/Rtmp6hdAbw/file3f782c6a2b54/ti:/ti" -v \
  "/d/Users/sandra.wiedenmann/AppData/Local/Temp/Rtmp6hdAbw/file3f78189f64f5/tmp:/tmp2" \
  "dynverse/ti_paga_tree:v0.9.9.04" --dataset /ti/input.h5 --output /ti/output.h5 --use_priors all
|

after a few hours I stopped it. when I let it once run over night it showed the Error:

Error: Error during trajectory inference Container was killed, possibly because it ran out of memory (error code 137)

I also tried other packages and a colleague of mine has exactly the same problem with another single cell data set.

Best Sandra

the session info:

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

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

other attached packages:
 [1] shiny_1.3.2           dplyr_0.8.3           Matrix_1.2-17         dyno_0.1.1            dynwrap_1.1.3        
 [6] dynplot_1.0.1         dynmethods_1.0.2      dynguidelines_1.0.0   dynfeature_1.0.0.9000 Seurat_3.0.1         

loaded via a namespace (and not attached):
  [1] backports_1.1.4     Hmisc_4.2-0         dyndimred_1.0.1     babelwhale_1.0.0    plyr_1.8.4         
  [6] igraph_1.2.4.1      lazyeval_0.2.2      sp_1.3-1            proxyC_0.1.5        splines_3.6.0      
 [11] listenv_0.7.0       ggplot2_3.2.0       digest_0.6.20       foreach_1.4.7       htmltools_0.3.6    
 [16] viridis_0.5.1       gdata_2.18.0        magrittr_1.5        checkmate_1.9.4     carrier_0.1.0      
 [21] cluster_2.0.8       ROCR_1.0-7          remotes_2.1.0       globals_0.12.4      readr_1.3.1        
 [26] RcppParallel_4.4.3  R.utils_2.9.0       dynutils_1.0.3      pdist_1.2           colorspace_1.4-1   
 [31] ggrepel_0.8.1       xfun_0.8            crayon_1.3.4        jsonlite_1.6        zeallot_0.1.0      
 [36] iterators_1.0.12    survival_2.44-1.1   zoo_1.8-6           ape_5.3             glue_1.3.1         
 [41] polyclip_1.10-0     gtable_0.3.0        future.apply_1.3.0  dynparam_1.0.0      scales_1.0.0       
 [46] bibtex_0.4.2        Rcpp_1.0.2          metap_1.1           viridisLite_0.3.0   xtable_1.8-4       
 [51] htmlTable_1.13.1    reticulate_1.13     bit_1.1-14          foreign_0.8-71      rsvd_1.0.2         
 [56] akima_0.6-2         SDMTools_1.1-221.1  Formula_1.2-3       tsne_0.1-3          htmlwidgets_1.3    
 [61] httr_1.4.1          FNN_1.1.3           gplots_3.0.1.1      RColorBrewer_1.1-2  acepack_1.4.1      
 [66] ica_1.0-2           pkgconfig_2.0.2     R.methodsS3_1.7.1   farver_1.1.0        nnet_7.3-12        
 [71] tidyselect_0.2.5    rlang_0.4.0         reshape2_1.4.3      later_0.8.0         munsell_0.5.0      
 [76] tools_3.6.0         cli_1.1.0           ranger_0.11.2       ggridges_0.5.1      stringr_1.4.0      
 [81] yaml_2.2.0          npsurv_0.4-0        bit64_0.9-7         processx_3.4.1      knitr_1.24         
 [86] fitdistrplus_1.0-14 tidygraph_1.1.2     caTools_1.17.1.2    purrr_0.3.2         RANN_2.6.1         
 [91] ggraph_1.0.2        pbapply_1.4-1       future_1.14.0       nlme_3.1-139        mime_0.7           
 [96] GA_3.2              R.oo_1.22.0         hdf5r_1.2.0         compiler_3.6.0      rstudioapi_0.10    
[101] plotly_4.9.0        png_0.1-7           testthat_2.2.1      lsei_1.2-0          tibble_2.1.3       
[106] tweenr_1.0.1        stringi_1.4.3       ps_1.3.0            lattice_0.20-38     shinyjs_1.0        
[111] vctrs_0.2.0         pillar_1.4.2        Rdpack_0.11-0       lmtest_0.9-37       data.table_1.12.2  
[116] cowplot_1.0.0       bitops_1.0-6        irlba_2.3.3         gbRd_0.4-11         patchwork_0.0.1    
[121] httpuv_1.5.1        R6_2.4.0            latticeExtra_0.6-28 promises_1.0.1      KernSmooth_2.23-15 
[126] gridExtra_2.3       codetools_0.2-16    MASS_7.3-51.4       gtools_3.8.1        assertthat_0.2.1   
[131] rje_1.9             shinyWidgets_0.4.8  sctransform_0.2.0   parallel_3.6.0      hms_0.5.0          
[136] grid_3.6.0          rpart_4.1-15        tidyr_0.8.3         Rtsne_0.15          ggforce_0.2.2      
[141] base64enc_0.1-3

dynverse / dyno

Error in "model <- infer_trajectory(dataset, methods_selected, verbose = TRUE)" #61