BiocParallel errors from muscat
1
0
Entering edit mode
tangming2005 ▴ 190
@tangming2005-6754
Last seen 3 months ago
United States

Hi there, I am using muscat for differential expression analysis for single-cell data, and I got the error below. what's wrong here?


 res<- pbDS(sce_pb, design = design, contrast = my.contrasts)
  |==================================================================================================================================================| 100%
Error: BiocParallel errors
  element index: 1, 2, 3, 4, 5, 6, ...
  first error: subscript out of bounds


 devtools::session_info()
─ Session info  ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 hash: eagle, pensive face, sweat droplets

 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       Ubuntu 20.04.3 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2022-03-23
 rstudio  2021.09.0+351 Ghost Orchid (server)
 pandoc   2.14.0.3 @ /usr/lib/rstudio-server/bin/pandoc/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date (UTC) lib source
 abind                  1.4-5      2016-07-21 [2] RSPM (R 4.1.0)
 annotate               1.70.0     2021-05-19 [1] Bioconductor
 AnnotationDbi          1.56.2     2021-11-09 [1] Bioconductor
 assertthat             0.2.1      2019-03-21 [2] RSPM (R 4.1.0)
 backports              1.3.0      2021-10-27 [2] RSPM (R 4.1.0)
 beachmat               2.8.1      2021-08-12 [1] Bioconductor
 beeswarm               0.4.0      2021-06-01 [1] RSPM (R 4.1.0)
 Biobase              * 2.54.0     2021-10-26 [1] Bioconductor
 BiocGenerics         * 0.40.0     2021-10-26 [1] Bioconductor
 BiocNeighbors          1.10.0     2021-05-19 [1] Bioconductor
 BiocParallel         * 1.26.2     2021-08-22 [1] Bioconductor
 BiocSingular           1.8.1      2021-06-08 [1] Bioconductor
 Biostrings             2.62.0     2021-10-26 [1] Bioconductor
 bit                    4.0.4      2020-08-04 [2] RSPM (R 4.1.0)
 bit64                  4.0.5      2020-08-30 [2] RSPM (R 4.1.0)
 bitops                 1.0-7      2021-04-24 [2] RSPM (R 4.1.0)
 blme                   1.0-5      2021-01-05 [1] RSPM (R 4.1.0)
 blob                   1.2.2      2021-07-23 [2] RSPM (R 4.1.0)
 boot                   1.3-28     2021-05-03 [3] CRAN (R 4.1.2)
 broom                  0.7.10     2021-10-31 [2] RSPM (R 4.1.0)
 cachem                 1.0.6      2021-08-19 [2] RSPM (R 4.1.0)
 callr                  3.7.0      2021-04-20 [2] RSPM (R 4.1.0)
 car                    3.0-12     2021-11-06 [1] RSPM (R 4.1.0)
 carData                3.0-5      2022-01-06 [1] RSPM (R 4.1.0)
 caTools                1.18.2     2021-03-28 [2] RSPM (R 4.1.0)
 cellranger             1.1.0      2016-07-27 [2] RSPM (R 4.1.0)
 circlize               0.4.13     2021-06-09 [1] RSPM (R 4.1.0)
 cli                    3.1.0      2021-10-27 [2] RSPM (R 4.1.0)
 clue                   0.3-60     2021-10-11 [1] RSPM (R 4.1.0)
 cluster                2.1.2      2021-04-17 [3] CRAN (R 4.1.2)
 codetools              0.2-18     2020-11-04 [3] CRAN (R 4.1.2)
 colorspace             2.0-2      2021-06-24 [2] RSPM (R 4.1.0)
 colorway               0.2.0      2022-02-10 [1] Github (hypercompetent/colorway@8ba8f00)
 ComplexHeatmap         2.10.0     2021-10-26 [1] Bioconductor
 cowplot                1.1.1      2020-12-30 [2] RSPM (R 4.1.0)
 crayon                 1.4.2      2021-10-29 [2] RSPM (R 4.1.0)
 data.table             1.14.2     2021-09-27 [2] RSPM (R 4.1.0)
 DBI                    1.1.1      2021-01-15 [2] RSPM (R 4.1.0)
 dbplyr                 2.1.1      2021-04-06 [2] RSPM (R 4.1.0)
 DelayedArray           0.18.0     2021-05-19 [1] Bioconductor
 DelayedMatrixStats     1.14.3     2021-08-26 [1] Bioconductor
 deldir                 1.0-6      2021-10-23 [2] RSPM (R 4.1.0)
 desc                   1.4.0      2021-09-28 [2] RSPM (R 4.1.0)
 DESeq2                 1.32.0     2021-05-19 [1] Bioconductor
 devtools               2.4.2      2021-06-07 [2] RSPM (R 4.1.0)
 digest                 0.6.28     2021-09-23 [2] RSPM (R 4.1.0)
 distributional         0.3.0      2022-01-05 [1] RSPM (R 4.1.0)
 dittoSeq               1.7.0      2022-02-10 [1] Github (dtm2451/dittoSeq@b158b29)
 doParallel             1.0.17     2022-02-07 [1] RSPM (R 4.1.0)
 dplyr                * 1.0.7      2021-06-18 [2] RSPM (R 4.1.0)
 edgeR                  3.34.1     2021-09-05 [1] Bioconductor
 ellipsis               0.3.2      2021-04-29 [2] RSPM (R 4.1.0)
 evaluate               0.14       2019-05-28 [2] RSPM (R 4.1.0)
 fansi                  0.5.0      2021-05-25 [2] RSPM (R 4.1.0)
 farver                 2.1.0      2021-02-28 [2] RSPM (R 4.1.0)
 fastmap                1.1.0      2021-01-25 [2] RSPM (R 4.1.0)
 fitdistrplus           1.1-6      2021-09-28 [2] RSPM (R 4.1.0)
 forcats              * 0.5.1      2021-01-27 [2] RSPM (R 4.1.0)
 foreach                1.5.2      2022-02-02 [1] RSPM (R 4.1.0)
 fs                     1.5.0      2020-07-31 [2] RSPM (R 4.1.0)
 future                 1.23.0     2021-10-31 [2] RSPM (R 4.1.0)
 future.apply           1.8.1      2021-08-10 [2] RSPM (R 4.1.0)
 genefilter             1.74.1     2021-10-12 [1] Bioconductor
 geneplotter            1.70.0     2021-05-19 [1] Bioconductor
 generics               0.1.1      2021-10-25 [2] RSPM (R 4.1.0)
 GenomeInfoDb         * 1.30.1     2022-01-30 [1] Bioconductor
 GenomeInfoDbData       1.2.7      2022-02-09 [1] Bioconductor
 GenomicRanges        * 1.44.0     2021-05-19 [1] Bioconductor
 GetoptLong             1.0.5      2020-12-15 [1] RSPM (R 4.1.0)
 ggbeeswarm             0.6.0      2017-08-07 [1] RSPM (R 4.1.0)
 ggdist                 3.1.0      2022-02-13 [1] RSPM (R 4.1.0)
 ggplot2              * 3.3.5      2021-06-25 [2] RSPM (R 4.1.0)
 ggprism                1.0.3.9000 2022-02-10 [1] Github (csdaw/ggprism@e21c3ee)
 ggpubr                 0.4.0      2020-06-27 [1] RSPM (R 4.1.0)
 ggrepel                0.9.1      2021-01-15 [2] RSPM (R 4.1.0)
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 ggsignif               0.6.3      2021-09-09 [1] RSPM (R 4.1.0)
 glmmTMB                1.1.3      2022-03-13 [1] RSPM (R 4.1.0)
 GlobalOptions          0.1.2      2020-06-10 [1] RSPM (R 4.1.0)
 globals                0.14.0     2020-11-22 [2] RSPM (R 4.1.0)
 glue                   1.5.0      2021-11-07 [2] RSPM (R 4.1.0)
 goftest                1.2-3      2021-10-07 [2] RSPM (R 4.1.0)
 gplots                 3.1.1      2020-11-28 [2] RSPM (R 4.1.0)
 gridExtra              2.3        2017-09-09 [2] RSPM (R 4.1.0)
 gtable                 0.3.0      2019-03-25 [2] RSPM (R 4.1.0)
 gtools                 3.9.2      2021-06-06 [2] RSPM (R 4.1.0)
 harmony              * 0.1.0      2021-06-02 [1] RSPM (R 4.1.2)
 haven                  2.4.3      2021-08-04 [2] RSPM (R 4.1.0)
 hdf5r                  1.3.5      2021-11-15 [1] RSPM (R 4.1.0)
 here                 * 1.0.1      2020-12-13 [2] RSPM (R 4.1.0)
 hms                    1.1.1      2021-09-26 [2] RSPM (R 4.1.0)
 htmltools              0.5.2      2021-08-25 [2] RSPM (R 4.1.0)
 htmlwidgets            1.5.4      2021-09-08 [2] RSPM (R 4.1.0)
 httpuv                 1.6.3      2021-09-09 [2] RSPM (R 4.1.0)
 httr                   1.4.2      2020-07-20 [2] RSPM (R 4.1.0)
 ica                    1.0-2      2018-05-24 [2] RSPM (R 4.1.0)
 igraph                 1.2.8      2021-11-07 [2] RSPM (R 4.1.0)
 IRanges              * 2.28.0     2021-10-26 [1] Bioconductor
 irlba                  2.3.3      2019-02-05 [2] RSPM (R 4.1.0)
 iterators              1.0.14     2022-02-05 [1] RSPM (R 4.1.0)
 janitor                2.1.0      2021-01-05 [1] RSPM (R 4.1.0)
 jsonlite               1.7.2      2020-12-09 [2] RSPM (R 4.1.0)
 KEGGREST               1.34.0     2021-10-26 [1] Bioconductor
 KernSmooth             2.23-20    2021-05-03 [3] CRAN (R 4.1.2)
 knitr                  1.36       2021-09-29 [2] RSPM (R 4.1.0)
 later                  1.3.0      2021-08-18 [2] RSPM (R 4.1.0)
 lattice                0.20-45    2021-09-22 [3] CRAN (R 4.1.2)
 lazyeval               0.2.2      2019-03-15 [2] RSPM (R 4.1.0)
 leiden                 0.3.9      2021-07-27 [2] RSPM (R 4.1.0)
 lifecycle              1.0.1      2021-09-24 [2] RSPM (R 4.1.0)
 limma                * 3.50.0     2021-10-26 [1] Bioconductor
 listenv                0.8.0      2019-12-05 [2] RSPM (R 4.1.0)
 lme4                   1.1-28     2022-02-05 [1] RSPM (R 4.1.0)
 lmerTest               3.1-3      2020-10-23 [1] RSPM (R 4.1.0)
 lmtest                 0.9-39     2021-11-07 [2] RSPM (R 4.1.0)
 locfit                 1.5-9.4    2020-03-25 [1] RSPM (R 4.1.0)
 lubridate              1.8.0      2021-10-07 [2] RSPM (R 4.1.0)
 magrittr               2.0.1      2020-11-17 [2] RSPM (R 4.1.0)
 MASS                   7.3-54     2021-05-03 [3] CRAN (R 4.1.2)
 Matrix                 1.3-4      2021-06-01 [3] CRAN (R 4.1.2)
 MatrixGenerics       * 1.4.3      2021-08-26 [1] Bioconductor
 matrixStats          * 0.61.0     2021-09-17 [2] RSPM (R 4.1.0)
 memoise                2.0.0      2021-01-26 [2] RSPM (R 4.1.0)
 mgcv                   1.8-38     2021-10-06 [3] CRAN (R 4.1.2)
 mime                   0.12       2021-09-28 [2] RSPM (R 4.1.0)
 miniUI                 0.1.1.1    2018-05-18 [2] RSPM (R 4.1.0)
 minqa                  1.2.4      2014-10-09 [1] RSPM (R 4.1.0)
 modelr                 0.1.8      2020-05-19 [2] RSPM (R 4.1.0)
 munsell                0.5.0      2018-06-12 [2] RSPM (R 4.1.0)
 muscat               * 1.8.2      2022-03-10 [1] Bioconductor
 nlme                   3.1-153    2021-09-07 [3] CRAN (R 4.1.2)
 nloptr                 2.0.0      2022-01-26 [1] RSPM (R 4.1.0)
 numDeriv               2016.8-1.1 2019-06-06 [1] RSPM (R 4.1.0)
 paletteer              1.4.0      2021-07-20 [1] RSPM (R 4.1.0)
 parallelly             1.28.1     2021-09-09 [2] RSPM (R 4.1.0)
 patchwork              1.1.1      2020-12-17 [2] RSPM (R 4.1.0)
 pbapply                1.5-0      2021-09-16 [2] RSPM (R 4.1.0)
 pbkrtest               0.5.1      2021-03-09 [1] RSPM (R 4.1.0)
 pheatmap               1.0.12     2019-01-04 [1] RSPM (R 4.1.0)
 pillar                 1.6.4      2021-10-18 [2] RSPM (R 4.1.0)
 pkgbuild               1.2.0      2020-12-15 [2] RSPM (R 4.1.0)
 pkgconfig              2.0.3      2019-09-22 [2] RSPM (R 4.1.0)
 pkgload                1.2.3      2021-10-13 [2] RSPM (R 4.1.0)
 plotly                 4.10.0     2021-10-09 [2] RSPM (R 4.1.0)
 plyr                   1.8.6      2020-03-03 [2] RSPM (R 4.1.0)
 png                    0.1-7      2013-12-03 [2] RSPM (R 4.1.0)
 polyclip               1.10-0     2019-03-14 [2] RSPM (R 4.1.0)
 presto                 1.0.0      2022-02-23 [1] Github (immunogenomics/presto@052085d)
 prettyunits            1.1.1      2020-01-24 [2] RSPM (R 4.1.0)
 processx               3.5.2      2021-04-30 [2] RSPM (R 4.1.0)
 progress               1.2.2      2019-05-16 [2] RSPM (R 4.1.0)
 promises               1.2.0.1    2021-02-11 [2] RSPM (R 4.1.0)
 ps                     1.6.0      2021-02-28 [2] RSPM (R 4.1.0)
 purrr                * 0.3.4      2020-04-17 [2] RSPM (R 4.1.0)
 R6                     2.5.1      2021-08-19 [2] RSPM (R 4.1.0)
 RANN                   2.6.1      2019-01-08 [2] RSPM (R 4.1.0)
 RColorBrewer           1.1-2      2014-12-07 [2] RSPM (R 4.1.0)
 Rcpp                 * 1.0.7      2021-07-07 [2] RSPM (R 4.1.0)
 RcppAnnoy              0.0.19     2021-07-30 [2] RSPM (R 4.1.0)
 RCurl                  1.98-1.6   2022-02-08 [1] RSPM (R 4.1.0)
 readr                * 2.1.0      2021-11-11 [2] RSPM (R 4.1.0)
 readxl                 1.3.1      2019-03-13 [2] RSPM (R 4.1.0)
 rematch2               2.1.2      2020-05-01 [2] RSPM (R 4.1.0)
 remotes                2.4.1      2021-09-29 [2] RSPM (R 4.1.0)
 reprex                 2.0.1      2021-08-05 [2] RSPM (R 4.1.0)
 reshape2               1.4.4      2020-04-09 [2] RSPM (R 4.1.0)
 reticulate             1.22       2021-09-17 [2] RSPM (R 4.1.0)
 rjson                  0.2.21     2022-01-09 [1] RSPM (R 4.1.0)
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 rstatix                0.7.0      2021-02-13 [1] RSPM (R 4.1.0)
 rstudioapi             0.13       2020-11-12 [2] RSPM (R 4.1.0)
 rsvd                   1.0.5      2021-04-16 [1] RSPM (R 4.1.0)
 Rtsne                  0.15       2018-11-10 [2] RSPM (R 4.1.0)
 rvest                  1.0.2      2021-10-16 [2] RSPM (R 4.1.0)
 S4Vectors            * 0.32.3     2021-11-21 [1] Bioconductor
 ScaledMatrix           1.0.0      2021-05-19 [1] Bioconductor
 scales                 1.1.1      2020-05-11 [2] RSPM (R 4.1.0)
 scater                 1.22.0     2021-10-26 [1] Bioconductor
 scattermore            0.7        2020-11-24 [2] RSPM (R 4.1.0)
 scCustomize          * 0.7.0      2022-02-10 [1] Github (samuel-marsh/scCustomize@8414d1f)
 sctransform            0.3.3      2022-01-13 [1] RSPM (R 4.1.0)
 scuttle                1.2.1      2021-08-05 [1] Bioconductor
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 Seurat               * 4.1.0      2022-01-14 [1] RSPM (R 4.1.0)
 SeuratDisk           * 0.0.0.9019 2022-02-10 [1] Github (mojaveazure/seurat-disk@163f1aa)
 SeuratObject         * 4.0.4      2021-11-23 [1] RSPM (R 4.1.0)
 shape                  1.4.6      2021-05-19 [1] RSPM (R 4.1.0)
 shiny                  1.7.1      2021-10-02 [2] RSPM (R 4.1.0)
 SingleCellExperiment * 1.14.1     2021-05-21 [1] Bioconductor
 snakecase              0.11.0     2019-05-25 [1] RSPM (R 4.1.0)
 sparseMatrixStats      1.4.2      2021-08-08 [1] Bioconductor
 SummarizedExperiment * 1.22.0     2021-05-19 [1] Bioconductor


 [1] /home/rstudio/R/x86_64-pc-linux-gnu-library/4.1-3.14
 [2] /usr/local/lib/R/site-library
 [3] /usr/local/lib/R/library

I also tried below before running pbDS. same error

library("BiocParallel")
registered()
serialParam <- SerialParam()
register(serialParam)

Thanks! Tommy

BiocParallel muscat single-cell • 262 views
ADD COMMENT
3
Entering edit mode
@martin-morgan-1513
Last seen 4 hours ago
United States

From the BiocParallel perspective, you could make some progress with

result <- bptry({
    pbDS(sce_pb, design = design, contrast = my.contrasts, BPPARAM = SerialParam())
})

and then discover the actual error and the 'traceback' illustrating where things have gone wrong

> result[[1]]
<remote_error in FUN(...): ...>
traceback() available as 'attr(x, "traceback")'
> traceback(result[[1]])
...

I would guess that one of the objects you are passing to pbDS() is not correct in some way, e.g., the design or contrasts specified incorrectly; perhaps there is a help page ?pbDS with an example that you could (a) run, so that you know that the function works in principle and (b) compare with for your specific objects?

ADD COMMENT
0
Entering edit mode

Thank you, Martin. Indeed, the design was wrong. it now works.

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