Augur runs only with toy data

[alicedini]

Hey, and thanks again for this package! I have been using it with no issues up until a few months ago, and after a break, I wanted to go back to using it for other projects, but I got stuck. Augur seems to stall with my data, but runs just fine with the toy data sc_sim. I tried using both Seurat objects or sparse matrices without success. I also converted the Seurat objects to v3 from v5, and I obtained the same results. Has there been any significant update that would have caused this?

Here is my sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-conda-linux-gnu
Running under: Red Hat Enterprise Linux 8.10 (Ootpa)

Matrix products: default
BLAS/LAPACK: /homedir01/adini22/.conda/envs/HDAC_project_augur_v2/lib/libopenblasp-r0.3.28.so; LAPACK version 3.12.0

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

time zone: Europe/Helsinki
tzcode source: system (glibc)

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

other attached packages:
[1] Matrix_1.7-1 randomForest_4.7-1.2 pbmcapply_1.5.1
[4] sparseMatrixStats_1.17.2 MatrixGenerics_1.19.0 matrixStats_1.4.1
[7] yardstick_1.3.1 recipes_1.1.0 rsample_1.2.1
[10] parsnip_1.2.1 magrittr_2.0.3 purrr_1.0.2
[13] tibble_3.2.1 dplyr_1.1.4 Seurat_5.0.3
[16] SeuratObject_5.0.2 sp_2.1-4 Augur_1.0.3

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.9 spatstat.utils_3.1-1
[4] farver_2.1.2 vctrs_0.6.5 ROCR_1.0-11
[7] spatstat.explore_3.3-3 base64enc_0.1-3 htmltools_0.5.8.1
[10] sctransform_0.4.1 parallelly_1.39.0 KernSmooth_2.23-24
[13] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9
[16] plotly_4.10.4 zoo_1.8-12 lubridate_1.9.3
[19] uuid_1.2-1 igraph_2.1.1 mime_0.12
[22] lifecycle_1.0.4 pkgconfig_2.0.3 R6_2.5.1
[25] fastmap_1.2.0 fitdistrplus_1.2-1 future_1.34.0
[28] shiny_1.9.1 digest_0.6.37 colorspace_2.1-1
[31] furrr_0.3.1 patchwork_1.3.0 tensor_1.5
[34] RSpectra_0.16-2 irlba_2.3.5.1 progressr_0.15.0
[37] spatstat.sparse_3.1-0 fansi_1.0.6 timechange_0.3.0
[40] polyclip_1.10-7 abind_1.4-8 httr_1.4.7
[43] compiler_4.4.1 fastDummies_1.7.4 maps_3.4.2.1
[46] MASS_7.3-61 lava_1.8.0 tools_4.4.1
[49] lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.3
[52] goftest_1.2-3 nnet_7.3-19 glue_1.8.0
[55] nlme_3.1-166 promises_1.3.0 grid_4.4.1
[58] pbdZMQ_0.3-13 Rtsne_0.17 cluster_2.1.6
[61] reshape2_1.4.4 generics_0.1.3 gtable_0.3.6
[64] spatstat.data_3.1-4 class_7.3-22 tidyr_1.3.1
[67] data.table_1.16.2 utf8_1.2.4 spatstat.geom_3.3-4
[70] RcppAnnoy_0.0.22 ggrepel_0.9.6 RANN_2.6.2
[73] pillar_1.9.0 stringr_1.5.1 spam_2.11-0
[76] IRdisplay_1.1 RcppHNSW_0.6.0 pals_1.9
[79] later_1.3.2 splines_4.4.1 lattice_0.22-6
[82] deldir_2.0-4 survival_3.7-0 tidyselect_1.2.1
[85] miniUI_0.1.1.1 pbapply_1.7-2 gridExtra_2.3
[88] scattermore_1.2 hardhat_1.4.0 timeDate_4041.110
[91] stringi_1.8.4 lazyeval_0.2.2 evaluate_1.0.1
[94] codetools_0.2-20 tester_0.2.0 cli_3.6.3
[97] uwot_0.2.2 IRkernel_1.3.2 rpart_4.1.23
[100] xtable_1.8-4 reticulate_1.40.0 repr_1.1.7
[103] munsell_0.5.1 dichromat_2.0-0.1 Rcpp_1.0.13-1
[106] spatstat.random_3.3-2 globals_0.16.3 mapproj_1.2.11
[109] png_0.1-8 spatstat.univar_3.1-1 gower_1.0.1
[112] ggplot2_3.5.1 dotCall64_1.2 listenv_0.9.1
[115] viridisLite_0.4.2 ipred_0.9-15 scales_1.3.0
[118] prodlim_2024.06.25 ggridges_0.5.6 leiden_0.4.3.1
[121] crayon_1.5.3 rlang_1.1.4 cowplot_1.1.3

Thank you for your help in advance!

[AlanTeoYueYang]

Hi, can you share your data with me?

[alicedini]

Thank you for the prompt response! How should I share the data with you?

[AlanTeoYueYang]

Can you send an email to [email protected]? I will provide a Dropbox link