search

HelenaLC / muscat

Multi-sample multi-group scRNA-seq analysis tools
166 stars 33 forks source link

pbDS takes very long time #42

Closed crazyhottommy closed 4 years ago

crazyhottommy commented 4 years ago

Hi Helen, Thanks for looking into this. It takes very long time (>24hours) and it is still running.

The rds file can be downloaded at https://drive.google.com/file/d/18DSW1vxUKl_7NWJI9Y-AEFWOC6H40CSr/view?usp=sharing

library(muscat)
library(limma)
library(here)
library(Seurat)
library(SingleCellExperiment)
library(purrr)
library(ggplot2)
library(readr)
library(ggrepel)

cd3_minus_pb<- readRDS(here("results/cd3_minus_pb.rds"))
colData(cd3_minus_pb)
design <- model.matrix(~0  + group_id, colData(cd3_minus_pb))
my.contrasts <- makeContrasts(
                              preCR_vs_prePD=group_idrefractory_CR_C1D1 - group_idrefractory_PD_C1D1,
                              levels=design)

res<- pbDS(cd3_minus_pb, design = design, contrast = my.contrasts,
                          verbose = TRUE, min_cells = 10, filter = "both")

session information:

> devtools::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       Ubuntu 20.04 LTS            
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Etc/UTC                     
 date     2020-08-21                  

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date       lib source                          
 abind                  1.4-5      2016-07-21 [2] RSPM (R 4.0.0)                  
 annotate               1.66.0     2020-04-27 [1] Bioconductor                    
 AnnotationDbi          1.50.3     2020-07-25 [1] Bioconductor                    
 ape                    5.4        2020-06-03 [1] RSPM (R 4.0.2)                  
 assertthat             0.2.1      2019-03-21 [2] RSPM (R 4.0.0)                  
 backports              1.1.8      2020-06-17 [2] RSPM (R 4.0.1)                  
 beeswarm               0.2.3      2016-04-25 [1] RSPM (R 4.0.0)                  
 Biobase              * 2.48.0     2020-04-27 [1] Bioconductor                    
 BiocGenerics         * 0.34.0     2020-04-27 [1] Bioconductor                    
 BiocNeighbors          1.6.0      2020-04-27 [1] Bioconductor                    
 BiocParallel           1.22.0     2020-04-27 [1] Bioconductor                    
 BiocSingular           1.4.0      2020-04-27 [1] Bioconductor                    
 bit                    1.1-15.2   2020-02-10 [2] RSPM (R 4.0.0)                  
 bit64                  0.9-7.1    2020-07-15 [2] RSPM (R 4.0.2)                  
 bitops                 1.0-6      2013-08-17 [1] RSPM (R 4.0.0)                  
 blme                   1.0-4      2015-06-14 [1] RSPM (R 4.0.0)                  
 blob                   1.2.1      2020-01-20 [2] RSPM (R 4.0.0)                  
 boot                   1.3-25     2020-04-26 [3] CRAN (R 4.0.2)                  
 callr                  3.4.3      2020-03-28 [2] RSPM (R 4.0.0)                  
 caTools                1.18.0     2020-01-17 [1] RSPM (R 4.0.0)                  
 circlize               0.4.10     2020-06-15 [1] RSPM (R 4.0.0)                  
 cli                    2.0.2      2020-02-28 [2] RSPM (R 4.0.0)                  
 clue                   0.3-57     2019-02-25 [1] RSPM (R 4.0.0)                  
 cluster                2.1.0      2019-06-19 [3] CRAN (R 4.0.2)                  
 codetools              0.2-16     2018-12-24 [3] CRAN (R 4.0.2)                  
 colorRamps             2.3        2012-10-29 [1] RSPM (R 4.0.0)                  
 colorspace             1.4-1      2019-03-18 [2] RSPM (R 4.0.0)                  
 ComplexHeatmap         2.4.3      2020-07-25 [1] Bioconductor                    
 cowplot                1.0.0      2019-07-11 [1] RSPM (R 4.0.0)                  
 crayon                 1.3.4      2017-09-16 [2] RSPM (R 4.0.0)                  
 data.table             1.13.0     2020-07-24 [2] RSPM (R 4.0.2)                  
 DBI                    1.1.0      2019-12-15 [2] RSPM (R 4.0.0)                  
 DelayedArray         * 0.14.1     2020-07-14 [1] Bioconductor                    
 DelayedMatrixStats     1.10.1     2020-07-03 [1] Bioconductor                    
 deldir                 0.1-28     2020-07-15 [2] RSPM (R 4.0.2)                  
 desc                   1.2.0      2018-05-01 [2] RSPM (R 4.0.0)                  
 DESeq2                 1.28.1     2020-05-12 [1] Bioconductor                    
 devtools               2.3.1      2020-07-21 [2] RSPM (R 4.0.2)                  
 digest                 0.6.25     2020-02-23 [2] RSPM (R 4.0.0)                  
 doParallel             1.0.15     2019-08-02 [1] RSPM (R 4.0.0)                  
 dplyr                  1.0.0      2020-05-29 [2] RSPM (R 4.0.0)                  
 edgeR                  3.30.3     2020-06-02 [1] Bioconductor                    
 ellipsis               0.3.1      2020-05-15 [2] RSPM (R 4.0.0)                  
 evaluate               0.14       2019-05-28 [2] RSPM (R 4.0.0)                  
 fansi                  0.4.1      2020-01-08 [2] RSPM (R 4.0.0)                  
 fastmap                1.0.1      2019-10-08 [2] RSPM (R 4.0.0)                  
 fitdistrplus           1.1-1      2020-05-19 [1] RSPM (R 4.0.0)                  
 foreach                1.5.0      2020-03-30 [2] RSPM (R 4.0.0)                  
 fs                     1.4.2      2020-06-30 [2] RSPM (R 4.0.2)                  
 future                 1.18.0     2020-07-09 [2] RSPM (R 4.0.2)                  
 future.apply           1.6.0      2020-07-01 [1] RSPM (R 4.0.2)                  
 gdata                  2.18.0     2017-06-06 [2] RSPM (R 4.0.0)                  
 genefilter             1.70.0     2020-04-27 [1] Bioconductor                    
 geneplotter            1.66.0     2020-04-27 [1] Bioconductor                    
 generics               0.0.2      2018-11-29 [2] RSPM (R 4.0.0)                  
 GenomeInfoDb         * 1.24.2     2020-06-15 [1] Bioconductor                    
 GenomeInfoDbData       1.2.3      2020-08-05 [1] Bioconductor                    
 GenomicRanges        * 1.40.0     2020-04-27 [1] Bioconductor                    
 GetoptLong             1.0.2      2020-07-06 [1] RSPM (R 4.0.2)                  
 ggbeeswarm             0.6.0      2017-08-07 [1] RSPM (R 4.0.0)                  
 ggplot2              * 3.3.2      2020-06-19 [2] RSPM (R 4.0.1)                  
 ggrepel              * 0.8.2      2020-03-08 [1] RSPM (R 4.0.2)                  
 ggridges               0.5.2      2020-01-12 [1] RSPM (R 4.0.0)                  
 glmmTMB                1.0.2.1    2020-07-02 [1] RSPM (R 4.0.2)                  
 GlobalOptions          0.1.2      2020-06-10 [1] RSPM (R 4.0.0)                  
 globals                0.12.5     2019-12-07 [2] RSPM (R 4.0.0)                  
 glue                   1.4.1      2020-05-13 [2] RSPM (R 4.0.0)                  
 goftest                1.2-2      2019-12-02 [2] RSPM (R 4.0.0)                  
 gplots                 3.0.4      2020-07-05 [1] RSPM (R 4.0.2)                  
 gridExtra              2.3        2017-09-09 [2] RSPM (R 4.0.0)                  
 gtable                 0.3.0      2019-03-25 [2] RSPM (R 4.0.0)                  
 gtools                 3.8.2      2020-03-31 [2] RSPM (R 4.0.0)                  
 here                 * 0.1        2017-05-28 [1] RSPM (R 4.0.0)                  
 hms                    0.5.3      2020-01-08 [2] RSPM (R 4.0.0)                  
 htmltools              0.5.0      2020-06-16 [2] RSPM (R 4.0.1)                  
 htmlwidgets            1.5.1      2019-10-08 [2] RSPM (R 4.0.0)                  
 httpuv                 1.5.4      2020-06-06 [2] RSPM (R 4.0.2)                  
 httr                   1.4.2      2020-07-20 [2] RSPM (R 4.0.2)                  
 ica                    1.0-2      2018-05-24 [1] RSPM (R 4.0.0)                  
 igraph                 1.2.5      2020-03-19 [1] RSPM (R 4.0.0)                  
 IRanges              * 2.22.2     2020-05-21 [1] Bioconductor                    
 irlba                  2.3.3      2019-02-05 [1] RSPM (R 4.0.0)                  
 iterators              1.0.12     2019-07-26 [2] RSPM (R 4.0.0)                  
 jsonlite               1.7.0      2020-06-25 [2] RSPM (R 4.0.2)                  
 KernSmooth             2.23-17    2020-04-26 [3] CRAN (R 4.0.2)                  
 knitr                  1.29       2020-06-23 [2] RSPM (R 4.0.2)                  
 later                  1.1.0.1    2020-06-05 [2] RSPM (R 4.0.2)                  
 lattice                0.20-41    2020-04-02 [3] CRAN (R 4.0.2)                  
 lazyeval               0.2.2      2019-03-15 [2] RSPM (R 4.0.0)                  
 leiden                 0.3.3      2020-02-04 [1] RSPM (R 4.0.0)                  
 lifecycle              0.2.0      2020-03-06 [2] RSPM (R 4.0.0)                  
 limma                * 3.44.3     2020-06-12 [1] Bioconductor                    
 listenv                0.8.0      2019-12-05 [2] RSPM (R 4.0.0)                  
 lme4                   1.1-23     2020-04-07 [1] RSPM (R 4.0.2)                  
 lmerTest               3.1-2      2020-04-08 [1] RSPM (R 4.0.0)                  
 lmtest                 0.9-37     2019-04-30 [1] RSPM (R 4.0.0)                  
 locfit                 1.5-9.4    2020-03-25 [1] RSPM (R 4.0.0)                  
 magrittr               1.5        2014-11-22 [2] RSPM (R 4.0.0)                  
 MASS                   7.3-51.6   2020-04-26 [3] CRAN (R 4.0.2)                  
 Matrix                 1.2-18     2019-11-27 [3] CRAN (R 4.0.2)                  
 matrixStats          * 0.56.0     2020-03-13 [1] RSPM (R 4.0.0)                  
 memoise                1.1.0      2017-04-21 [2] RSPM (R 4.0.0)                  
 mgcv                   1.8-31     2019-11-09 [3] CRAN (R 4.0.2)                  
 mime                   0.9        2020-02-04 [2] RSPM (R 4.0.0)                  
 miniUI                 0.1.1.1    2018-05-18 [2] RSPM (R 4.0.0)                  
 minqa                  1.2.4      2014-10-09 [1] RSPM (R 4.0.2)                  
 munsell                0.5.0      2018-06-12 [2] RSPM (R 4.0.0)                  
 muscat               * 1.2.1      2020-08-05 [1] Github (HelenaLC/muscat@02e3833)
 nlme                   3.1-148    2020-05-24 [3] CRAN (R 4.0.2)                  
 nloptr                 1.2.2.2    2020-07-02 [1] RSPM (R 4.0.2)                  
 numDeriv               2016.8-1.1 2019-06-06 [1] RSPM (R 4.0.0)                  
 packrat                0.5.0      2018-11-14 [2] RSPM (R 4.0.0)                  
 patchwork              1.0.1      2020-06-22 [1] RSPM (R 4.0.2)                  
 pbapply                1.4-2      2019-08-31 [1] RSPM (R 4.0.0)                  
 pbkrtest               0.4-8.6    2020-02-20 [1] RSPM (R 4.0.0)                  
 pillar                 1.4.6      2020-07-10 [2] RSPM (R 4.0.2)                  
 pkgbuild               1.1.0      2020-07-13 [2] RSPM (R 4.0.2)                  
 pkgconfig              2.0.3      2019-09-22 [2] RSPM (R 4.0.0)                  
 pkgload                1.1.0      2020-05-29 [2] RSPM (R 4.0.0)                  
 plotly                 4.9.2.1    2020-04-04 [1] RSPM (R 4.0.0)                  
 plyr                   1.8.6      2020-03-03 [2] RSPM (R 4.0.2)                  
 png                    0.1-7      2013-12-03 [2] RSPM (R 4.0.0)                  
 polyclip               1.10-0     2019-03-14 [2] RSPM (R 4.0.0)                  
 prettyunits            1.1.1      2020-01-24 [2] RSPM (R 4.0.0)                  
 processx               3.4.3      2020-07-05 [2] RSPM (R 4.0.2)                  
 progress               1.2.2      2019-05-16 [2] RSPM (R 4.0.0)                  
 promises               1.1.1      2020-06-09 [2] RSPM (R 4.0.2)                  
 ps                     1.3.3      2020-05-08 [2] RSPM (R 4.0.0)                  
 purrr                * 0.3.4      2020-04-17 [2] RSPM (R 4.0.0)                  
 R6                     2.4.1      2019-11-12 [2] RSPM (R 4.0.0)                  
 RANN                   2.6.1      2019-01-08 [1] RSPM (R 4.0.0)                  
 rappdirs               0.3.1      2016-03-28 [1] RSPM (R 4.0.0)                  
 RColorBrewer           1.1-2      2014-12-07 [2] RSPM (R 4.0.0)                  
 Rcpp                   1.0.5      2020-07-06 [2] RSPM (R 4.0.2)                  
 RcppAnnoy              0.0.16     2020-03-08 [1] RSPM (R 4.0.2)                  
 RCurl                  1.98-1.2   2020-04-18 [1] RSPM (R 4.0.0)                  
 readr                * 1.3.1      2018-12-21 [2] RSPM (R 4.0.2)                  
 remotes                2.2.0      2020-07-21 [2] RSPM (R 4.0.2)                  
 reshape2               1.4.4      2020-04-09 [1] RSPM (R 4.0.2)                  
 reticulate             1.16       2020-05-27 [1] RSPM (R 4.0.2)                  
 rjson                  0.2.20     2018-06-08 [1] RSPM (R 4.0.0)                  
 rlang                  0.4.7      2020-07-09 [2] RSPM (R 4.0.2)                  
 rmarkdown              2.3        2020-06-18 [2] RSPM (R 4.0.1)                  
 ROCR                   1.0-11     2020-05-02 [1] RSPM (R 4.0.0)                  
 rpart                  4.1-15     2019-04-12 [3] CRAN (R 4.0.2)                  
 rprojroot              1.3-2      2018-01-03 [2] RSPM (R 4.0.0)                  
 RSQLite                2.2.0      2020-01-07 [2] RSPM (R 4.0.2)                  
 rstudioapi             0.11       2020-02-07 [2] RSPM (R 4.0.0)                  
 rsvd                   1.0.3      2020-02-17 [1] RSPM (R 4.0.0)                  
 Rtsne                  0.15       2018-11-10 [1] RSPM (R 4.0.2)                  
 S4Vectors            * 0.26.1     2020-05-16 [1] Bioconductor                    
 scales                 1.1.1      2020-05-11 [2] RSPM (R 4.0.0)                  
 scater                 1.16.2     2020-06-26 [1] Bioconductor                    
 sctransform            0.2.1      2019-12-17 [1] RSPM (R 4.0.2)                  
 sessioninfo            1.1.1      2018-11-05 [2] RSPM (R 4.0.0)                  
 Seurat               * 3.2.0      2020-07-16 [1] RSPM (R 4.0.2)                  
 shape                  1.4.4      2018-02-07 [1] RSPM (R 4.0.0)                  
 shiny                  1.5.0      2020-06-23 [2] RSPM (R 4.0.2)                  
 SingleCellExperiment * 1.10.1     2020-04-28 [1] Bioconductor                    
 spatstat               1.64-1     2020-05-12 [2] RSPM (R 4.0.0)                  
 spatstat.data          1.4-3      2020-01-26 [2] RSPM (R 4.0.0)                  
 spatstat.utils         1.17-0     2020-02-07 [2] RSPM (R 4.0.0)                  
 statmod                1.4.34     2020-02-17 [1] RSPM (R 4.0.0)                  
 stringi                1.4.6      2020-02-17 [2] RSPM (R 4.0.0)                  
 stringr                1.4.0      2019-02-10 [2] RSPM (R 4.0.0)                  
 SummarizedExperiment * 1.18.2     2020-07-09 [1] Bioconductor                    
 survival               3.1-12     2020-04-10 [3] CRAN (R 4.0.2)                  
 tensor                 1.5        2012-05-05 [2] RSPM (R 4.0.0)                  
 testthat               2.3.2      2020-03-02 [2] RSPM (R 4.0.0)                  
 tibble                 3.0.3      2020-07-10 [2] RSPM (R 4.0.2)                  
 tidyr                  1.1.0      2020-05-20 [2] RSPM (R 4.0.2)                  
 tidyselect             1.1.0      2020-05-11 [2] RSPM (R 4.0.0)                  
 TMB                    1.7.18     2020-07-27 [1] RSPM (R 4.0.2)                  
 usethis                1.6.1      2020-04-29 [2] RSPM (R 4.0.0)                  
 uwot                   0.1.8      2020-03-16 [1] RSPM (R 4.0.2)                  
 variancePartition      1.18.3     2020-08-07 [1] Bioconductor                    
 vctrs                  0.3.2      2020-07-15 [2] RSPM (R 4.0.2)                  
 vipor                  0.4.5      2017-03-22 [1] RSPM (R 4.0.0)                  
 viridis                0.5.1      2018-03-29 [2] RSPM (R 4.0.0)                  
 viridisLite            0.3.0      2018-02-01 [2] RSPM (R 4.0.0)                  
 withr                  2.2.0      2020-04-20 [2] RSPM (R 4.0.0)                  
 xfun                   0.16       2020-07-24 [2] RSPM (R 4.0.2)                  
 XML                    3.99-0.5   2020-07-23 [2] RSPM (R 4.0.2)                  
 xtable                 1.8-4      2019-04-21 [2] RSPM (R 4.0.0)                  
 XVector                0.28.0     2020-04-27 [1] Bioconductor                    
 yaml                   2.2.1      2020-02-01 [2] RSPM (R 4.0.0)                  
 zlibbioc               1.34.0     2020-04-27 [1] Bioconductor                    
 zoo                    1.8-8      2020-05-02 [2] RSPM (R 4.0.0)                  

[1] /homes6/mtang/R/x86_64-pc-linux-gnu-library/4.0
[2] /usr/local/lib/R/site-library
[3] /usr/local/lib/R/library
crazyhottommy commented 4 years ago

somehow it is only taking long time if I submit a slurm job (using singularity). If I run interactively, it finished in a reasonable time. closing it for now.