jgranja24
commented
4 years ago Ok im looking into this, can you try with 1 thread and see if the issue is still present.
Closed HYsxe closed 4 years ago
jgranja24
commented
4 years ago Ok im looking into this, can you try with 1 thread and see if the issue is still present.
HYsxe
commented
4 years ago Thanks for your response! Running the code on 1 thread indeed solved my problem! So I suppose this is a parallelization problem? Is there a way for me to successfully run on multiple cores? Thank you!
rcorces
commented
4 years ago The problems with parallelization are very system specific and we have not fully addressed this. It is on our radar but I'm closing this issue.
rootze
commented
3 years ago Hello, I run into a similar problem and it didn't get solved by using threads = 1
doubScores <- addDoubletScores(
input = ArrowFiles,
k = 10,
knnMethod = "UMAP",
LSIMethod = 1,
threads=1
)The following is the error message and log, ArchR-addDoubletScores-62c51b14d496-Date-2021-07-23_Time-17-09-31.log
OW_1 (8 of 9) : Correlation of UMAP Projection is below 0.9 (normally this is ~0.99)
This means there is little heterogeneity in your sample and thus doubletCalling is inaccurate.
force = FALSE, thus returning -1 doubletScores and doubletEnrichments!
Set force = TRUE if you want to continue (not recommended).
2021-07-23 17:24:06 : FW_1 (9 of 9) : Computing Doublet Statistics, 14.568 mins elapsed.
Warning in irlba::irlba(mat, nDimensions, nDimensions) :
You're computing too large a percentage of total singular values, use a standard svd instead.
Warning: The following arguments are not used: row.names
************************************************************
2021-07-23 17:24:14 : ERROR Found in FindClusters for
LogFile = ArchRLogs/ArchR-addDoubletScores-62c51b14d496-Date-2021-07-23_Time-17-09-31.log
<simpleError in sample.int(length(x), size, replace, prob): invalid first argument>
************************************************************
************************************************************
2021-07-23 17:24:14 : ERROR Found in runClusters for
LogFile = ArchRLogs/ArchR-addDoubletScores-62c51b14d496-Date-2021-07-23_Time-17-09-31.log
<simpleError in .logError(e, fn = "FindClusters", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
************************************************************
************************************************************
2021-07-23 17:24:14 : ERROR Found in .LSICluster for
LogFile = ArchRLogs/ArchR-addDoubletScores-62c51b14d496-Date-2021-07-23_Time-17-09-31.log
<simpleError in .logError(e, fn = "runClusters", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
************************************************************
************************************************************
2021-07-23 17:24:14 : ERROR Found in addIterativeLSI for FW_1 (9 of 9) :
LogFile = ArchRLogs/ArchR-addDoubletScores-62c51b14d496-Date-2021-07-23_Time-17-09-31.log
<simpleError: $ operator is invalid for atomic vectors>
************************************************************
Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), :
Exiting See Error Above
In addition: Warning messages:
1: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
2: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
3: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
4: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
5: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
6: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
7: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
8: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
>
I'm new to this, and I didn't run into any problems with TutorialData Please help me out. Thank you!
rcorces
commented
3 years ago @rootze - please clarify if you encounter this error using the tutorial dataset and tutorial code
rootze
commented
3 years ago @rootze - please clarify if you encounter this error using the tutorial dataset and tutorial code
Thank you for your reply. No, I didn't encounter this error with the tutorial code and dataset.
rcorces
commented
3 years ago @rootze - Your error is not related to the original poster's error. Your error is coming from Seurat's FindClusters function. Originally I had thought there might be some incompatibility between your version of Seurat and ArchR but that doesnt appear to be the case if the tutorial works fine for you. I have a feeling that there is something specific to your dataset that is causing the error and that isnt easy for me to troubleshoot.
rootze
commented
3 years ago @rcorces Thank you for your analysis. The dataset is from my PI. He also provided me the ArrowFiles he made with "DoubletScore" and "DoubletEnrichment" in cellColData. And he provided me with his code as well. But for some reason, he can get addDoubletScores() working. This is the part that confused me the most. Originally I thought there is something wrong with the dataset, but my PI's code works, and at the same time, the ArchR code works fine on the Tutorial dataset under current Conda environment. By the way, I used ArchR in Conda environment on HPC. The following is the sessionInfo().
Maybe, I should make a new ArchR only Conda environment on HPC?
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /data/homezvol0/zechuas/.conda/envs/R_scATAC/lib/libopenblasp-r0.3.15.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] patchwork_1.1.1 SeuratObject_4.0.2
[3] Seurat_4.0.3 Signac_1.2.1
[5] Rmagic_2.0.3 ArchR_1.0.1
[7] magrittr_2.0.1 rhdf5_2.36.0
[9] Matrix_1.3-4 data.table_1.14.0
[11] SummarizedExperiment_1.22.0 Biobase_2.52.0
[13] GenomicRanges_1.44.0 GenomeInfoDb_1.28.1
[15] IRanges_2.26.0 S4Vectors_0.30.0
[17] BiocGenerics_0.38.0 MatrixGenerics_1.4.0
[19] matrixStats_0.59.0 ggplot2_3.3.5
loaded via a namespace (and not attached):
[1] fastmatch_1.1-0 plyr_1.8.6 igraph_1.2.6
[4] lazyeval_0.2.2 splines_4.1.0 BiocParallel_1.26.1
[7] listenv_0.8.0 scattermore_0.7 SnowballC_0.7.0
[10] digest_0.6.27 htmltools_0.5.1.1 fansi_0.5.0
[13] tensor_1.5 cluster_2.1.2 ROCR_1.0-11
[16] globals_0.14.0 Biostrings_2.60.1 docopt_0.7.1
[19] spatstat.sparse_2.0-0 colorspace_2.0-2 rappdirs_0.3.3
[22] ggrepel_0.9.1 dplyr_1.0.7 sparsesvd_0.2
[25] crayon_1.4.1 RCurl_1.98-1.3 jsonlite_1.7.2
[28] spatstat.data_2.1-0 survival_3.2-11 zoo_1.8-9
[31] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0
[34] zlibbioc_1.38.0 XVector_0.32.0 leiden_0.3.8
[37] DelayedArray_0.18.0 Rhdf5lib_1.14.2 future.apply_1.7.0
[40] abind_1.4-5 scales_1.1.1 DBI_1.1.1
[43] miniUI_0.1.1.1 Rcpp_1.0.7 viridisLite_0.4.0
[46] xtable_1.8-4 reticulate_1.20 spatstat.core_2.2-0
[49] htmlwidgets_1.5.3 httr_1.4.2 RColorBrewer_1.1-2
[52] ellipsis_0.3.2 ica_1.0-2 pkgconfig_2.0.3
[55] farver_2.1.0 ggseqlogo_0.1 uwot_0.1.10
[58] deldir_0.2-10 utf8_1.2.1 tidyselect_1.1.1
[61] rlang_0.4.11 reshape2_1.4.4 later_1.2.0
[64] munsell_0.5.0 tools_4.1.0 generics_0.1.0
[67] ggridges_0.5.3 stringr_1.4.0 fastmap_1.1.0
[70] goftest_1.2-2 fitdistrplus_1.1-5 purrr_0.3.4
[73] RANN_2.6.1 pbapply_1.4-3 future_1.21.0
[76] nlme_3.1-152 mime_0.11 slam_0.1-48
[79] RcppRoll_0.3.0 compiler_4.1.0 rstudioapi_0.13
[82] plotly_4.9.4.1 png_0.1-7 spatstat.utils_2.2-0
[85] tibble_3.1.2 tweenr_1.0.2 stringi_1.6.2
[88] lattice_0.20-44 vctrs_0.3.8 pillar_1.6.1
[91] lifecycle_1.0.0 rhdf5filters_1.4.0 spatstat.geom_2.2-0
[94] lmtest_0.9-38 RcppAnnoy_0.0.18 cowplot_1.1.1
[97] bitops_1.0-7 irlba_2.3.3 httpuv_1.6.1
[100] R6_2.5.0 promises_1.2.0.1 KernSmooth_2.23-20
[103] gridExtra_2.3 lsa_0.73.2 parallelly_1.26.1
[106] codetools_0.2-18 MASS_7.3-54 assertthat_0.2.1
[109] withr_2.4.2 qlcMatrix_0.9.7 sctransform_0.3.2
[112] Rsamtools_2.8.0 GenomeInfoDbData_1.2.6 mgcv_1.8-36
[115] grid_4.1.0 rpart_4.1-15 tidyr_1.1.3
[118] Cairo_1.5-12.2 Rtsne_0.15 ggforce_0.3.3
[121] shiny_1.6.0Sorry - I dont have much to add here. Sounds like an environment-specific problem. You'll have to troubleshoot on your end.
tanasa
commented
2 years ago Hey folks, I am getting a similar error. I was wondering whether we have found a solution in the meanwhile to the same problem. Thank you.
> doubScores <- addDoubletScores(
+ input = ArrowFiles,
+ k = 10,
+ knnMethod = "UMAP",
+ LSIMethod = 1,
+ threads=1
+ )
ArchR logging to : ArchRLogs/ArchR-addDoubletScores-bd0b115ab860-Date-2022-03-24_Time-10-09-11.log
If there is an issue, please report to github with logFile!
2022-03-24 10:09:11 : Batch Execution w/ safelapply!, 0 mins elapsed.
2022-03-24 10:09:11 : scATAC (1 of 1) : Computing Doublet Statistics, 0 mins elapsed.
************************************************************
2022-03-24 10:09:16 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addDoubletScores-bd0b115ab860-Date-2022-03-24_Time-10-09-11.log
<simpleError in irlba::irlba(mat, nDimensions, nDimensions): max(nu, nv) must be strictly less than min(nrow(A), ncol(A))>
************************************************************
************************************************************
2022-03-24 10:09:16 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-bd0b115ab860-Date-2022-03-24_Time-10-09-11.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
************************************************************
************************************************************
2022-03-24 10:09:16 : ERROR Found in addIterativeLSI for scATAC (1 of 1) :
LogFile = ArchRLogs/ArchR-addDoubletScores-bd0b115ab860-Date-2022-03-24_Time-10-09-11.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
************************************************************
Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), :
Exiting See Error Above> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] gridExtra_2.3 Rsamtools_2.10.0
[3] BSgenome.Hsapiens.UCSC.hg38_1.4.4 BSgenome_1.62.0
[5] rtracklayer_1.54.0 Biostrings_2.62.0
[7] XVector_0.34.0 ArchR_1.0.1
[9] magrittr_2.0.2 rhdf5_2.38.1
[11] Matrix_1.4-0 data.table_1.14.2
[13] SummarizedExperiment_1.24.0 Biobase_2.54.0
[15] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[17] IRanges_2.28.0 S4Vectors_0.32.3
[19] BiocGenerics_0.40.0 MatrixGenerics_1.6.0
[21] matrixStats_0.61.0 ggplot2_3.3.5
[23] SeuratData_0.2.1 SeuratObject_4.0.4
[25] Seurat_4.1.0 fgsea_1.20.0
[27] BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] fastmatch_1.1-3 plyr_1.8.6 igraph_1.2.11
[4] lazyeval_0.2.2 splines_4.1.3 BiocParallel_1.28.3
[7] listenv_0.8.0 scattermore_0.8 usethis_2.1.5
[10] digest_0.6.29 htmltools_0.5.2 fansi_1.0.2
[13] memoise_2.0.1 tensor_1.5 cluster_2.1.2
[16] ROCR_1.0-11 remotes_2.4.2 globals_0.14.0
[19] spatstat.sparse_2.1-0 prettyunits_1.1.1 colorspace_2.0-3
[22] rappdirs_0.3.3 ggrepel_0.9.1 dplyr_1.0.8
[25] callr_3.7.0 crayon_1.5.0 RCurl_1.98-1.6
[28] jsonlite_1.8.0 spatstat.data_2.1-2 survival_3.3-1
[31] zoo_1.8-9 glue_1.6.2 polyclip_1.10-0
[34] gtable_0.3.0 zlibbioc_1.40.0 leiden_0.3.9
[37] DelayedArray_0.20.0 pkgbuild_1.3.1 Rhdf5lib_1.16.0
[40] future.apply_1.8.1 abind_1.4-5 scales_1.1.1
[43] DBI_1.1.2 spatstat.random_2.1-0 miniUI_0.1.1.1
[46] Rcpp_1.0.8.3 viridisLite_0.4.0 xtable_1.8-4
[49] reticulate_1.24 spatstat.core_2.4-0 htmlwidgets_1.5.4
[52] httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2
[55] ica_1.0-2 farver_2.1.0 XML_3.99-0.9
[58] pkgconfig_2.0.3 uwot_0.1.11 deldir_1.0-6
[61] utf8_1.2.2 labeling_0.4.2 tidyselect_1.1.2
[64] rlang_1.0.2 reshape2_1.4.4 later_1.3.0
[67] munsell_0.5.0 tools_4.1.3 cachem_1.0.6
[70] cli_3.2.0 generics_0.1.2 devtools_2.4.3
[73] ggridges_0.5.3 stringr_1.4.0 fastmap_1.1.0
[76] yaml_2.3.5 goftest_1.2-3 processx_3.5.2
[79] fs_1.5.2 fitdistrplus_1.1-8 purrr_0.3.4
[82] RANN_2.6.1 pbapply_1.5-0 future_1.24.0
[85] nlme_3.1-155 mime_0.12 brio_1.1.3
[88] compiler_4.1.3 plotly_4.10.0 curl_4.3.2
[91] png_0.1-7 testthat_3.1.2 spatstat.utils_2.3-0
[94] tibble_3.1.6 stringi_1.7.6 ps_1.6.0
[97] desc_1.4.1 lattice_0.20-45 vctrs_0.3.8
[100] rhdf5filters_1.6.0 pillar_1.7.0 lifecycle_1.0.1
[103] spatstat.geom_2.3-2 lmtest_0.9-40 RcppAnnoy_0.0.19
[106] cowplot_1.1.1 bitops_1.0-7 irlba_2.3.5
[109] httpuv_1.6.5 patchwork_1.1.1 BiocIO_1.4.0
[112] R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20
[115] parallelly_1.30.0 sessioninfo_1.2.2 codetools_0.2-18
[118] MASS_7.3-56 pkgload_1.2.4 rjson_0.2.21
[121] rprojroot_2.0.2 withr_2.5.0 GenomicAlignments_1.30.0
[124] sctransform_0.3.3 GenomeInfoDbData_1.2.7 mgcv_1.8-39
[127] parallel_4.1.3 rpart_4.1.16 tidyr_1.2.0
[130] Cairo_1.5-15 Rtsne_0.15 shiny_1.7.1
[133] restfulr_0.0.13 @tanasa Hi, not sure if this will work for you. After I had that problem, I tried to set my whole ArchR thread to 1 for addDoubletScores. But it failed for some reason since my ArrowFiles are not generated under 1 thread. So I re-generated the ArrowFiles, but this time I set my whole ArchR thread to 1, which solved my problem, and addDoubletScores worked as well. Maybe give it a try?
addArchRThreads(1)
ZunpengLiu
commented
2 years ago Hi folks,
I also encounter this error. According to your suggestions, I re-generated the Arrowfiles and re-run the addDoubletScores with addArchRThreads(1). However, It still does not work for me. I still encounter the error as follows
************************************************************
2022-10-02 02:18:33 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addDoubletScores-2f2bd1c0e0be9-Date-2022-10-02_Time-02-18-27.log
<simpleError in irlba::irlba(mat, nDimensions, nDimensions): max(nu, nv) must be strictly less than min(nrow(A), ncol(A))>
************************************************************
************************************************************
2022-10-02 02:18:33 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-2f2bd1c0e0be9-Date-2022-10-02_Time-02-18-27.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
************************************************************
************************************************************
2022-10-02 02:18:33 : ERROR Found in addIterativeLSI for D19-122591 (1 of 1) :
LogFile = ArchRLogs/ArchR-addDoubletScores-2f2bd1c0e0be9-Date-2022-10-02_Time-02-18-27.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
************************************************************
Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), :
Exiting See Error Above
Thank you!
Zunpeng
hira-anis
commented
8 months ago was anyone able to answer this, please? I have the same error.
ArchR logging to : ArchRLogs/ArchR-addDoubletScores-1c023895e69e-Date-2024-02-22_Time-16-29-35.log If there is an issue, please report to github with logFile! 2024-02-22 16:29:35 : Batch Execution w/ safelapply!, 0 mins elapsed. 2024-02-22 16:29:35 : 7041_bloodasc (1 of 5) : Computing Doublet Statistics, 0 mins elapsed.
2024-02-22 16:29:46 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addDoubletScores-1c023895e69e-Date-2024-02-22_Time-16-29-35.log
<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>
2024-02-22 16:29:46 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-1c023895e69e-Date-2024-02-22_Time-16-29-35.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-02-22 16:29:46 : ERROR Found in addIterativeLSI for sample1 (1 of 5) :
LogFile = ArchRLogs/ArchR-addDoubletScores-1c023895e69e-Date-2024-02-22_Time-16-29-35.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), : Exiting See Error Above
─ Session info ─────────────────────────────────────────────────────────────────────── setting value version R version 4.2.3 (2023-03-15) os macOS Big Sur 11.0.1 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2024-02-22 rstudio 2023.03.0+386 Cherry Blossom (desktop) pandoc 2.11.3.2 @ /usr/local/bin/pandoc
─ Packages ─────────────────────────────────────────────────────────────────────────── package version date (UTC) lib source ArchR 1.0.3 2023-11-08 [1] Github (GreenleafLab/ArchR@65968a4) Biobase 2.58.0 2022-11-01 [1] Bioconductor BiocGenerics 0.44.0 2022-11-01 [1] Bioconductor BiocIO 1.8.0 2022-11-01 [1] Bioconductor BiocManager 1.30.22 2023-08-08 [1] CRAN (R 4.2.0) BiocParallel 1.32.6 2023-03-17 [1] Bioconductor Biostrings 2.66.0 2022-11-01 [1] Bioconductor bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0) BSgenome 1.66.3 2023-02-16 [1] Bioconductor BSgenome.Hsapiens.UCSC.hg38 1.4.5 2023-07-11 [1] Bioconductor cachem 1.0.8 2023-05-01 [1] CRAN (R 4.2.0) Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.2.3) cli 3.6.2 2023-12-11 [1] CRAN (R 4.2.3) codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.3) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0) data.table 1.15.0 2024-01-30 [1] CRAN (R 4.2.3) DelayedArray 0.24.0 2022-11-01 [1] Bioconductor devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.0) digest 0.6.34 2024-01-11 [1] CRAN (R 4.2.3) dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.2.3) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.2.3) farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.0) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0) fs 1.6.3 2023-07-20 [1] CRAN (R 4.2.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) GenomeInfoDb 1.34.9 2023-02-02 [1] Bioconductor GenomeInfoDbData 1.2.9 2023-03-26 [1] Bioconductor GenomicAlignments 1.34.1 2023-03-09 [1] Bioconductor GenomicRanges 1.50.2 2022-12-16 [1] Bioconductor ggplot2 3.4.4 2023-10-12 [1] CRAN (R 4.2.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.2.3) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0) gtable 0.3.4 2023-08-21 [1] CRAN (R 4.2.0) gtools 3.9.5 2023-11-20 [1] CRAN (R 4.2.3) htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.2.3) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.2.3) httpuv 1.6.14 2024-01-26 [1] CRAN (R 4.2.3) IRanges 2.32.0 2022-11-01 [1] Bioconductor irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.0) labeling 0.4.3 2023-08-29 [1] CRAN (R 4.2.0) later 1.3.2 2023-12-06 [1] CRAN (R 4.2.3) lattice 0.22-5 2023-10-24 [1] CRAN (R 4.2.3) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.2.3) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) MASS 7.3-60.0.1 2024-01-13 [1] CRAN (R 4.2.3) Matrix 1.6-4 2023-11-30 [1] CRAN (R 4.2.0) MatrixGenerics 1.10.0 2022-11-01 [1] Bioconductor matrixStats 1.2.0 2023-12-11 [1] CRAN (R 4.2.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0) 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) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.0) pkgbuild 1.4.3 2023-12-10 [1] CRAN (R 4.2.3) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.2.3) plyr 1.8.9 2023-10-02 [1] CRAN (R 4.2.0) profvis 0.3.8 2023-05-02 [1] CRAN (R 4.2.0) promises 1.2.1 2023-08-10 [1] CRAN (R 4.2.0) purrr 1.0.2 2023-08-10 [1] CRAN (R 4.2.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.2.3) RcppArmadillo 0.12.6.6.1 2023-12-04 [1] CRAN (R 4.2.0) RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.2.3) remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.2.0) restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.2.0) rhdf5 2.42.1 2023-04-07 [1] Bioconductor rhdf5filters 1.10.1 2023-03-24 [1] Bioconductor Rhdf5lib 1.20.0 2022-11-01 [1] Bioconductor rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0) rlang 1.1.3 2024-01-10 [1] CRAN (R 4.2.3) Rsamtools 2.14.0 2022-11-01 [1] Bioconductor RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.2.0) rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.2.0) rtracklayer 1.58.0 2022-11-01 [1] Bioconductor S4Vectors 0.36.2 2023-02-26 [1] Bioconductor scales 1.3.0 2023-11-28 [1] CRAN (R 4.2.3) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) shiny 1.8.0 2023-11-17 [1] CRAN (R 4.2.3) sparseMatrixStats 1.10.0 2022-11-01 [1] Bioconductor stringi 1.8.3 2023-12-11 [1] CRAN (R 4.2.3) stringr 1.5.1 2023-11-14 [1] CRAN (R 4.2.3) SummarizedExperiment 1.28.0 2022-11-01 [1] Bioconductor tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0) tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0) usethis 2.2.2 2023-07-06 [1] CRAN (R 4.2.0) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.2.3) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.2.3) withr 3.0.0 2024-01-16 [1] CRAN (R 4.2.3) XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.2.3) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0) XVector 0.38.0 2022-11-01 [1] Bioconductor yaml 2.3.8 2023-12-11 [1] CRAN (R 4.2.3) zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
NayeliGutierrez
commented
2 weeks ago Hi,
I am running the ArchR tutorial with the provided dataset and encountered the same error. I set threads = 1 both in the function argument and using the addArchRThreads function (both together and independently), but the issue persists. Please advise! I have attached the log and details.
Thank you!
`> addArchRThreads(threads = 1) Setting default number of Parallel threads to 1.
doubScores <- addDoubletScores(
- input = ArrowFiles,
- k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
- knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search.
- LSIMethod = 1,
- threads = 1
- ) ArchR logging to : ArchRLogs/ArchR-addDoubletScores-3ab1b23601025-Date-2024-09-30_Time-11-28-28.log If there is an issue, please report to github with logFile! 2024-09-30 11:28:28 : Batch Execution w/ safelapply!, 0 mins elapsed. 2024-09-30 11:28:28 : scATAC_BMMC_R1 (1 of 3) : Computing Doublet Statistics, 0 mins elapsed.
2024-09-30 11:28:34 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addDoubletScores-3ab1b23601025-Date-2024-09-30_Time-11-28-28.log
<simpleError in irlba::irlba(mat, nDimensions, nDimensions): function 'as_cholmod_sparse' not provided by package 'Matrix'>
2024-09-30 11:28:34 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-3ab1b23601025-Date-2024-09-30_Time-11-28-28.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
2024-09-30 11:28:34 : ERROR Found in addIterativeLSI for scATAC_BMMC_R1 (1 of 3) :
LogFile = ArchRLogs/ArchR-addDoubletScores-3ab1b23601025-Date-2024-09-30_Time-11-28-28.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), : Exiting See Error Above`
Session info:
`> sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Rocky Linux 9.4 (Blue Onyx)
Matrix products: default BLAS: /hpc/packages/minerva-rocky9/R/4.2.0/lib64/R/lib/libRblas.so LAPACK: /hpc/packages/minerva-rocky9/R/4.2.0/lib64/R/lib/libRlapack.so
Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets [9] methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.66.3
[3] rtracklayer_1.58.0 Biostrings_2.66.0
[5] XVector_0.38.0 SeuratObject_5.0.2
[7] sp_2.1-4 chromVAR_1.20.2
[9] rhdf5_2.42.1 SummarizedExperiment_1.28.0
[11] Biobase_2.58.0 MatrixGenerics_1.16.0
[13] Rcpp_1.0.13 Matrix_1.6-5
[15] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[17] IRanges_2.32.0 S4Vectors_0.36.2
[19] BiocGenerics_0.44.0 matrixStats_1.4.1
[21] data.table_1.16.0 stringr_1.5.1
[23] plyr_1.8.9 magrittr_2.0.3
[25] ggplot2_3.5.1 gtable_0.3.5
[27] gtools_3.9.5 gridExtra_2.3
[29] ArchR_1.0.2
loaded via a namespace (and not attached):
[1] colorspace_2.1-1 rjson_0.2.23
[3] rstudioapi_0.16.0 listenv_0.9.1
[5] DT_0.33 bit64_4.0.5
[7] AnnotationDbi_1.60.2 fansi_1.0.6
[9] codetools_0.2-18 R.methodsS3_1.8.2
[11] cachem_1.1.0 spam_2.10-0
[13] jsonlite_1.8.9 Rsamtools_2.14.0
[15] Cairo_1.6-2 seqLogo_1.64.0
[17] annotate_1.76.0 GO.db_3.16.0
[19] png_0.1-8 R.oo_1.26.0
[21] shiny_1.9.1 readr_2.1.5
[23] compiler_4.2.0 httr_1.4.7
[25] fastmap_1.2.0 lazyeval_0.2.2
[27] cli_3.6.3 later_1.3.2
[29] htmltools_0.5.8.1 tools_4.2.0
[31] dotCall64_1.1-1 glue_1.7.0
[33] TFMPvalue_0.0.9 GenomeInfoDbData_1.2.9
[35] reshape2_1.4.4 dplyr_1.1.4
[37] vctrs_0.6.5 rhdf5filters_1.10.1
[39] progressr_0.14.0 CNEr_1.34.0
[41] globals_0.16.3 irlba_2.3.5.1
[43] mime_0.12 miniUI_0.1.1.1
[45] lifecycle_1.0.4 restfulr_0.0.15
[47] poweRlaw_0.80.0 XML_3.99-0.17
[49] future_1.34.0 zlibbioc_1.44.0
[51] scales_1.3.0 hms_1.1.3
[53] promises_1.3.0 yaml_2.3.10
[55] memoise_2.0.1 stringi_1.8.4
[57] RSQLite_2.3.7 BiocIO_1.8.0
[59] caTools_1.18.3 BiocParallel_1.32.6
[61] rlang_1.1.4 pkgconfig_2.0.3
[63] bitops_1.0-8 pracma_2.4.4
[65] lattice_0.20-45 purrr_1.0.2
[67] Rhdf5lib_1.20.0 GenomicAlignments_1.34.1
[69] htmlwidgets_1.6.4 bit_4.0.5
[71] tidyselect_1.2.1 parallelly_1.38.0
[73] R6_2.5.1 generics_0.1.3
[75] DelayedArray_0.24.0 DBI_1.2.3
[77] pillar_1.9.0 withr_3.0.1
[79] KEGGREST_1.38.0 RCurl_1.98-1.16
[81] tibble_3.2.1 future.apply_1.11.2
[83] crayon_1.5.3 utf8_1.2.4
[85] plotly_4.10.4 tzdb_0.4.0
[87] TFBSTools_1.36.0 blob_1.2.4
[89] digest_0.6.37 xtable_1.8-4
[91] tidyr_1.3.1 httpuv_1.6.15
[93] R.utils_2.12.3 munsell_0.5.1
[95] DirichletMultinomial_1.40.0 viridisLite_0.4.2`
ArchR-addDoubletScores-3ab1b23601025-Date-2024-09-30_Time-11-28-28.log
Hi! I was running the tutorial code on tutorial data but couldn't get past doublet scoring. I keep seeing this error. Could you help have a look? Thanks!
This is the log file ArchR-addDoubletScores-acf5bf6df8c-Date-2020-06-19_Time-13-50-48.log
To Reproduce This is the code I used