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yuchaojiang / TRIPOD

Nonparametric Interrogation of Transcriptional Regulation in Single-Cell RNA and Chromatin Accessibility Multiomic Data
GNU General Public License v3.0
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Error: BiocParallel errors #4

Closed matteozoia4 closed 1 year ago

matteozoia4 commented 1 year ago

Dear TRIPOD providers,

while running step 5.1 Fitting models on my data : 

library(TRIPOD)
library(Seurat)
library(Signac)
library(GenomicRanges)
library(dplyr)
library(ggplot2)
library(EnsDb.Mmusculus.v79)
library(GenomeInfoDb)
library(patchwork)
library(BiocParallel)
library(dendextend)

load("transcripts.gr.rda")
load("peaks.gr.rda")
load("motifxTF.rda")
load("peakxmotif.rda")
load("metacell.rna.rda")
load("metacell.peak.rda")
load("metacell.celltype.rda")
load("metacell.celltype.col.rda")

genes <- c("Sox10", "Hcn1")
ext.upstream <- ext.downstream <- 5e5
xymats.list <- bplapply(
  genes,
  getXYMatrices,
  ext.upstream = ext.upstream,
  transcripts.gr = transcripts.gr,
  peaks.gr = peaks.gr,
  metacell.rna = metacell.rna,
  metacell.peak = metacell.peak,
  peakxmotif = peakxmotif,
  motifxTF = motifxTF,
  metacell.celltype = metacell.celltype,
  metacell.celltype.col = metacell.celltype.col
)
names(xymats.list) <- genes

I encounter this error : 

Error: BiocParallel errors
  6 remote errors, element index: 1, 2, 3, 4, 5, 6
  0 unevaluated and other errors
  first remote error:
Error in metacell.peak[, overlapsAny(peaks.gr, transcripts.ext.gr[transcripts.ext.gr$gene_name == : (subscript) logical subscript too long

Doest this have to do with character features that should be set as factor? How should I proceed in this case to identify which one is causing the error? I am of course available to share the data I am using in a confidential manner if needed to debug/solve the issue.

Many thanks in advance and a happy new year!

MZ


─ R Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.1 (2022-06-23)
 os       macOS Monterey 12.0.1
 system   x86_64, darwin17.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Zurich
 date     2023-01-04
 rstudio  2022.07.1+554 Spotted Wakerobin (desktop)
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package                          * version     date (UTC) lib source
 abind                              1.4-5       2016-07-21 [1] CRAN (R 4.2.0)
 ade4                               1.7-20      2022-11-01 [1] CRAN (R 4.2.0)
 annotate                           1.74.0      2022-04-26 [1] Bioconductor
 AnnotationDbi                    * 1.58.0      2022-04-26 [1] Bioconductor
 AnnotationFilter                 * 1.20.0      2022-04-26 [1] Bioconductor
 ArchR                            * 1.0.2       2022-09-13 [1] Github (GreenleafLab/ArchR@79953a9)
 askpass                            1.1         2019-01-13 [1] CRAN (R 4.2.0)
 assertthat                         0.2.1       2019-03-21 [1] CRAN (R 4.2.0)
 backports                          1.4.1       2021-12-13 [1] CRAN (R 4.2.0)
 base64enc                          0.1-3       2015-07-28 [1] CRAN (R 4.2.0)
 beachmat                           2.12.0      2022-04-26 [1] Bioconductor
 beeswarm                           0.4.0       2021-06-01 [1] CRAN (R 4.2.0)
 Biobase                          * 2.56.0      2022-04-26 [1] Bioconductor
 BiocFileCache                    * 2.4.0       2022-04-26 [1] Bioconductor
 BiocGenerics                     * 0.42.0      2022-04-26 [1] Bioconductor
 BiocIO                             1.6.0       2022-04-26 [1] Bioconductor
 BiocManager                      * 1.30.19     2022-10-25 [1] CRAN (R 4.2.0)
 BiocNeighbors                      1.14.0      2022-04-26 [1] Bioconductor
 BiocParallel                     * 1.30.4      2022-10-13 [1] Bioconductor
 BiocSingular                       1.12.0      2022-04-26 [1] Bioconductor
 biomaRt                            2.52.0      2022-04-26 [1] Bioconductor
 Biostrings                       * 2.64.1      2022-08-18 [1] Bioconductor
 biovizBase                       * 1.44.0      2022-04-26 [1] Bioconductor
 bit                                4.0.4       2020-08-04 [1] CRAN (R 4.2.0)
 bit64                              4.0.5       2020-08-30 [1] CRAN (R 4.2.0)
 bitops                             1.0-7       2021-04-24 [1] CRAN (R 4.2.0)
 blob                               1.2.3       2022-04-10 [1] CRAN (R 4.2.0)
 bluster                            1.6.0       2022-04-26 [1] Bioconductor
 BSgenome                         * 1.64.0      2022-04-26 [1] Bioconductor
 BSgenome.Mmusculus.UCSC.mm10     * 1.4.3       2022-09-13 [1] Bioconductor
 cachem                             1.0.6       2021-08-19 [1] CRAN (R 4.2.0)
 Cairo                              1.6-0       2022-07-05 [1] CRAN (R 4.2.0)
 callr                              3.7.3       2022-11-02 [1] CRAN (R 4.2.0)
 car                                3.1-1       2022-10-19 [1] CRAN (R 4.2.0)
 carData                            3.0-5       2022-01-06 [1] CRAN (R 4.2.0)
 caTools                            1.18.2      2021-03-28 [1] CRAN (R 4.2.0)
 checkmate                          2.1.0       2022-04-21 [1] CRAN (R 4.2.0)
 chromVAR                         * 1.18.0      2022-04-26 [1] Bioconductor
 circlize                           0.4.15      2022-05-10 [1] CRAN (R 4.2.0)
 cli                                3.4.1       2022-09-23 [1] CRAN (R 4.2.0)
 clue                               0.3-62      2022-10-18 [1] CRAN (R 4.2.0)
 cluster                            2.1.4       2022-08-22 [1] CRAN (R 4.2.0)
 CNEr                               1.32.0      2022-04-26 [1] Bioconductor
 codetools                          0.2-18      2020-11-04 [1] CRAN (R 4.2.1)
 colorspace                         2.0-3       2022-02-21 [1] CRAN (R 4.2.0)
 ComplexHeatmap                     2.12.1      2022-08-09 [1] Bioconductor
 cowplot                            1.1.1       2020-12-30 [1] CRAN (R 4.2.0)
 crayon                             1.5.2       2022-09-29 [1] CRAN (R 4.2.0)
 curl                               4.3.3       2022-10-06 [1] CRAN (R 4.2.0)
 data.table                       * 1.14.4      2022-10-17 [1] CRAN (R 4.2.0)
 DBI                                1.1.3       2022-06-18 [1] CRAN (R 4.2.0)
 dbplyr                           * 2.2.1       2022-06-27 [1] CRAN (R 4.2.0)
 DelayedArray                       0.22.0      2022-04-26 [1] Bioconductor
 DelayedMatrixStats                 1.18.2      2022-10-13 [1] Bioconductor
 deldir                             1.0-6       2021-10-23 [1] CRAN (R 4.2.0)
 dendextend                       * 1.16.0      2022-07-04 [1] CRAN (R 4.2.0)
 devtools                         * 2.4.5       2022-10-11 [1] CRAN (R 4.2.0)
 dichromat                          2.0-0.1     2022-05-02 [1] CRAN (R 4.2.0)
 digest                             0.6.30      2022-10-18 [1] CRAN (R 4.2.0)
 DirichletMultinomial               1.38.0      2022-04-26 [1] Bioconductor
 doParallel                         1.0.17      2022-02-07 [1] CRAN (R 4.2.0)
 dplyr                            * 1.0.99.9000 2022-11-09 [1] Github (tidyverse/dplyr@50c58dd)
 dqrng                              0.3.0       2021-05-01 [1] CRAN (R 4.2.0)
 DT                                 0.26        2022-10-19 [1] CRAN (R 4.2.0)
 edgeR                              3.38.4      2022-08-07 [1] Bioconductor
 ellipsis                           0.3.2       2021-04-29 [1] CRAN (R 4.2.0)
 EnsDb.Mmusculus.v79              * 2.99.0      2022-04-28 [1] Bioconductor
 ensembldb                        * 2.20.2      2022-06-21 [1] Bioconductor
 fansi                              1.0.3       2022-03-24 [1] CRAN (R 4.2.0)
 farver                             2.1.1       2022-07-06 [1] CRAN (R 4.2.0)
 fastmap                            1.1.0       2021-01-25 [1] CRAN (R 4.2.0)
 fastmatch                          1.1-3       2021-07-23 [1] CRAN (R 4.2.0)
 filelock                           1.0.2       2018-10-05 [1] CRAN (R 4.2.0)
 fitdistrplus                       1.1-8       2022-03-10 [1] CRAN (R 4.2.0)
 FNN                                1.1.3.1     2022-05-23 [1] CRAN (R 4.2.0)
 foreach                            1.5.2       2022-02-02 [1] CRAN (R 4.2.0)
 foreign                            0.8-83      2022-09-28 [1] CRAN (R 4.2.0)
 Formula                          * 1.2-4       2020-10-16 [1] CRAN (R 4.2.0)
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 future                             1.29.0      2022-11-06 [1] CRAN (R 4.2.1)
 future.apply                       1.10.0      2022-11-05 [1] CRAN (R 4.2.1)
 generics                           0.1.3       2022-07-05 [1] CRAN (R 4.2.0)
 GenomeInfoDb                     * 1.32.4      2022-09-06 [1] Bioconductor
 GenomeInfoDbData                   1.2.8       2022-04-23 [1] Bioconductor
 GenomicAlignments                  1.32.1      2022-08-02 [1] Bioconductor
 GenomicFeatures                  * 1.48.4      2022-09-20 [1] Bioconductor
 GenomicRanges                    * 1.48.0      2022-04-26 [1] Bioconductor
 GetoptLong                         1.0.5       2020-12-15 [1] CRAN (R 4.2.0)
 ggbeeswarm                         0.6.0       2017-08-07 [1] CRAN (R 4.2.0)
 ggplot2                          * 3.4.0       2022-11-04 [1] CRAN (R 4.2.0)
 ggrepel                            0.9.2       2022-11-06 [1] CRAN (R 4.2.1)
 ggridges                           0.5.4       2022-09-26 [1] CRAN (R 4.2.0)
 glmnet                             4.1-4       2022-04-15 [1] CRAN (R 4.2.0)
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 globals                            0.16.1      2022-08-28 [1] CRAN (R 4.2.0)
 glue                               1.6.2       2022-02-24 [1] CRAN (R 4.2.0)
 GO.db                              3.15.0      2022-05-12 [1] Bioconductor
 goftest                            1.2-3       2021-10-07 [1] CRAN (R 4.2.0)
 gridExtra                        * 2.3         2017-09-09 [1] CRAN (R 4.2.0)
 gtable                           * 0.3.1       2022-09-01 [1] CRAN (R 4.2.0)
 gtools                           * 3.9.3       2022-07-11 [1] CRAN (R 4.2.0)
 hdf5r                            * 1.3.7       2022-10-03 [1] CRAN (R 4.2.0)
 here                               1.0.1       2020-12-13 [1] CRAN (R 4.2.0)
 hexbin                           * 1.28.2      2021-01-08 [1] CRAN (R 4.2.0)
 Hmisc                            * 4.7-1       2022-08-15 [1] CRAN (R 4.2.0)
 hms                                1.1.2       2022-08-19 [1] CRAN (R 4.2.0)
 htmlTable                          2.4.1       2022-07-07 [1] CRAN (R 4.2.0)
 htmltools                          0.5.3       2022-07-18 [1] CRAN (R 4.2.0)
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 ica                                1.0-3       2022-07-08 [1] CRAN (R 4.2.0)
 igraph                             1.3.5       2022-09-22 [1] CRAN (R 4.2.0)
 interp                             1.1-3       2022-07-13 [1] CRAN (R 4.2.0)
 IRanges                          * 2.30.1      2022-08-18 [1] Bioconductor
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 JASPAR2020                       * 0.99.10     2022-04-28 [1] Bioconductor
 JASPAR2022                       * 0.99.7      2022-03-23 [1] Bioconductor
 jpeg                               0.1-9       2021-07-24 [1] CRAN (R 4.2.0)
 jsonlite                           1.8.3       2022-10-21 [1] CRAN (R 4.2.0)
 KEGGREST                           1.36.3      2022-07-14 [1] Bioconductor
 KernSmooth                         2.23-20     2021-05-03 [1] CRAN (R 4.2.1)
 knitr                              1.40        2022-08-24 [1] CRAN (R 4.2.0)
 labeling                           0.4.2       2020-10-20 [1] CRAN (R 4.2.0)
 later                              1.3.0       2021-08-18 [1] CRAN (R 4.2.0)
 lattice                          * 0.20-45     2021-09-22 [1] CRAN (R 4.2.1)
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 limma                              3.52.4      2022-09-27 [1] Bioconductor
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 lmtest                             0.9-40      2022-03-21 [1] CRAN (R 4.2.0)
 locfit                             1.5-9.6     2022-07-11 [1] CRAN (R 4.2.0)
 lubridate                          1.9.0       2022-11-06 [1] CRAN (R 4.2.1)
 magick                           * 2.7.3       2021-08-18 [1] CRAN (R 4.2.0)
 magrittr                         * 2.0.3       2022-03-30 [1] CRAN (R 4.2.0)
 MASS                               7.3-58.1    2022-08-03 [1] CRAN (R 4.2.0)
 mathjaxr                           1.6-0       2022-02-28 [1] CRAN (R 4.2.0)
 Matrix                           * 1.5-1       2022-09-13 [1] CRAN (R 4.2.0)
 MatrixGenerics                   * 1.8.1       2022-06-26 [1] Bioconductor
 matrixStats                      * 0.62.0      2022-04-19 [1] CRAN (R 4.2.0)
 mclust                             6.0.0       2022-10-31 [1] CRAN (R 4.2.0)
 memoise                            2.0.1       2021-11-26 [1] CRAN (R 4.2.0)
 metap                            * 1.8         2022-02-10 [1] CRAN (R 4.2.0)
 metapod                            1.4.0       2022-04-26 [1] Bioconductor
 mime                               0.12        2021-09-28 [1] CRAN (R 4.2.0)
 miniUI                             0.1.1.1     2018-05-18 [1] CRAN (R 4.2.0)
 mnormt                             2.1.1       2022-09-26 [1] CRAN (R 4.2.0)
 motifmatchr                      * 1.18.0      2022-04-26 [1] Bioconductor
 multcomp                           1.4-20      2022-08-07 [1] CRAN (R 4.2.0)
 multtest                         * 2.52.0      2022-04-26 [1] Bioconductor
 munsell                            0.5.0       2018-06-12 [1] CRAN (R 4.2.0)
 mutoss                             0.1-12      2017-12-04 [1] CRAN (R 4.2.0)
 mvtnorm                            1.1-3       2021-10-08 [1] CRAN (R 4.2.0)
 nabor                              0.5.0       2018-07-11 [1] CRAN (R 4.2.0)
 nbpMatching                        1.5.1       2016-04-19 [1] CRAN (R 4.2.0)
 nlme                               3.1-160     2022-10-10 [1] CRAN (R 4.2.0)
 nloptr                           * 2.0.3       2022-05-26 [1] CRAN (R 4.2.0)
 nnet                               7.3-18      2022-09-28 [1] CRAN (R 4.2.0)
 nortest                            1.0-4       2015-07-30 [1] CRAN (R 4.2.0)
 numDeriv                           2016.8-1.1  2019-06-06 [1] CRAN (R 4.2.0)
 olsrr                              0.5.3       2020-02-10 [1] CRAN (R 4.2.0)
 openssl                            2.0.4       2022-10-17 [1] CRAN (R 4.2.0)
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 patchwork                        * 1.1.2       2022-08-19 [1] CRAN (R 4.2.0)
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 pkgconfig                          2.0.3       2019-09-22 [1] CRAN (R 4.2.0)
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 plotly                             4.10.1      2022-11-07 [1] CRAN (R 4.2.1)
 plotrix                            3.8-2       2021-09-08 [1] CRAN (R 4.2.0)
 plyr                             * 1.8.7       2022-03-24 [1] CRAN (R 4.2.0)
 png                                0.1-7       2013-12-03 [1] CRAN (R 4.2.0)
 polyclip                           1.10-4      2022-10-20 [1] CRAN (R 4.2.0)
 poweRlaw                           0.70.6      2020-04-25 [1] CRAN (R 4.2.0)
 pracma                             2.4.2       2022-09-22 [1] CRAN (R 4.2.0)
 prettyunits                        1.1.1       2020-01-24 [1] CRAN (R 4.2.0)
 processx                           3.8.0       2022-10-26 [1] CRAN (R 4.2.0)
 profvis                            0.3.7       2020-11-02 [1] CRAN (R 4.2.0)
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 promises                           1.2.0.1     2021-02-11 [1] CRAN (R 4.2.0)
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 R6                                 2.5.1       2021-08-19 [1] CRAN (R 4.2.0)
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 RColorBrewer                       1.1-3       2022-04-03 [1] CRAN (R 4.2.0)
 Rcpp                             * 1.0.9       2022-07-08 [1] CRAN (R 4.2.0)
 RcppAnnoy                          0.0.20      2022-10-27 [1] CRAN (R 4.2.0)
 RcppRoll                           0.3.0       2018-06-05 [1] CRAN (R 4.2.0)
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 [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
yuchaojiang commented 1 year ago

Hi,

Thanks for your interest in TRIPOD.

I think it would be easiest if you can share with me the rda files that you loaded at the beginning. Of course, these will be kept strictly confidential.

yuchaojiang commented 1 year ago

Feel free to directly email me the data/link to data at yuchaoj at unc dot email dot edu. Thanks

yuchaojiang commented 1 year ago

Hi, the metacell.rna matrix that you sent contains all NaN. Double check how that is generated? It seems that your data is from mouse. Here is the most appropriate vignettes http://htmlpreview.github.io/?https://github.com/yuchaojiang/TRIPOD/blob/main/vignettes/preprocessing_e18.html

Let me know if you need more help

matteozoia4 commented 1 year ago

Many thanks I will check this out!

Yes it is from Mouse.

Matteo Zoia, Ph.D. Student Gene Regulation & Cardiac Development Osterwalder Lab Department for BioMedical Research (DBMR) University of Bern Murtenstrasse 28, 369 CH - 3008 Bern SWITZERLAND

Da: Yuchao Jiang @.***> Inviato: venerdì, 6. gennaio 2023 17:34:03 A: yuchaojiang/TRIPOD Cc: Zoia, Matteo (DBMR); Author Oggetto: Re: [yuchaojiang/TRIPOD] Error: BiocParallel errors (Issue #4)

Hi, the metacell.rna matrix that you sent contains all NaN. Double check how that is generated? It seems that your data is from mouse. Here is the most appropriate vignettes http://htmlpreview.github.io/?https://github.com/yuchaojiang/TRIPOD/blob/main/vignettes/preprocessing_e18.html

Let me know if you need more help

— Reply to this email directly, view it on GitHubhttps://github.com/yuchaojiang/TRIPOD/issues/4#issuecomment-1373871271, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUBHT3BKOBSHFAWIONKNLGTWRBCPXANCNFSM6AAAAAATQ3UCSE. You are receiving this because you authored the thread.Message ID: @.***>