Open Nichal123 opened 6 months ago
I have the same issue too, could anyone help?
Hi @Nichal123 , thank you for using harmony! I think the Seurat.ipynb vignette you refer to is part of the seurat documentation. Could you provide a link to it so we can take a look at it?
Hi @hongchengyao, thank you for your reply. The vignette I refer to is part of the Symphony documentation Link: https://github.com/immunogenomics/symphony/blob/main/vignettes/Seurat.ipynb.
Hi all,
I am trying to reproduce the Seurat.ipynb vignette to construct a reference object from a seurat object. However, I am encountering errors already from the Harmony step. The error I get: Error in value[3L] : Invalid number of ncores provided: 0. Maximum available cores: 64 It seems like not all parameters are passed (in the harmonymatrix function, ncores should be present, but it is not in 'utils_seurat.R'. I have tried to input the parameters that should be there (.options is missing and causing problems as well), but then Harmony is not running correctly (cell embedings, feature.loadings are all zero) Do I miss something?
Thanks in advance!
SESSION INFO R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS
Matrix products: default BLAS/LAPACK: /opt/OpenBLAS/lib/libopenblasp-r0.3.13.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] Matrix_1.6-4 magrittr_2.0.3 hcabm40k.SeuratData_3.0.0 SeuratData_0.2.2.9001 symphony_0.1.1
[6] patchwork_1.2.0 reshape2_1.4.4 dplyr_1.1.4 sctransform_0.4.1 aws.s3_0.3.21
[11] clustree_0.5.1 ggraph_2.1.0 ggplot2_3.4.4 harmony_1.2.0 Rcpp_1.0.12
[16] SeuratDisk_0.0.0.9021 Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-2
loaded via a namespace (and not attached): [1] utf8_1.2.4 spatstat.explore_3.2-5 reticulate_1.34.0 tidyselect_1.2.0 htmlwidgets_1.6.4
[6] grid_4.2.2 Rtsne_0.17 devtools_2.4.5 aws.signature_0.6.0 munsell_0.5.0
[11] codetools_0.2-18 ica_1.0-3 future_1.29.0 miniUI_0.1.1.1 withr_2.5.2
[16] spatstat.random_3.2-2 colorspace_2.1-0 progressr_0.14.0 knitr_1.45 rstudioapi_0.14
[21] stats4_4.2.2 ROCR_1.0-11 SparkR_3.3.1 tensor_1.5 listenv_0.9.0
[26] MatrixGenerics_1.10.0 labeling_0.4.3 polyclip_1.10-6 bit64_4.0.5 farver_2.1.1
[31] rprojroot_2.0.4 parallelly_1.36.0 vctrs_0.6.5 generics_0.1.3 xfun_0.41
[36] R6_2.5.1 graphlayouts_1.0.2 hdf5r_1.3.8 spatstat.utils_3.0-4 cachem_1.0.8
[41] promises_1.2.1 scales_1.3.0 gtable_0.3.4 globals_0.16.2 processx_3.8.0
[46] goftest_1.2-3 spam_2.10-0 tidygraph_1.3.0 rlang_1.1.2 splines_4.2.2
[51] lazyeval_0.2.2 spatstat.geom_3.2-7 abind_1.4-5 httpuv_1.6.13 usethis_2.1.6
[56] tools_4.2.2 ellipsis_0.3.2 RColorBrewer_1.1-3 BiocGenerics_0.44.0 sessioninfo_1.2.2
[61] ggridges_0.5.5 plyr_1.8.9 base64enc_0.1-3 purrr_1.0.2 ps_1.7.2
[66] prettyunits_1.2.0 deldir_2.0-2 pbapply_1.7-2 viridis_0.6.4 cowplot_1.1.2
[71] urlchecker_1.0.1 S4Vectors_0.36.2 zoo_1.8-12 ggrepel_0.9.4 cluster_2.1.4
[76] fs_1.6.3 data.table_1.14.10 RSpectra_0.16-1 scattermore_1.2 lmtest_0.9-40
[81] RANN_2.6.1 fitdistrplus_1.1-11 matrixStats_1.2.0 pkgload_1.3.1 hms_1.1.3
[86] mime_0.12 evaluate_0.23 xtable_1.8-4 RhpcBLASctl_0.23-42 fastDummies_1.7.3
[91] IRanges_2.32.0 gridExtra_2.3 compiler_4.2.2 tibble_3.2.1 KernSmooth_2.23-20
[96] crayon_1.5.2 htmltools_0.5.7 later_1.3.2 tzdb_0.4.0 tidyr_1.3.0
[101] tweenr_2.0.2 MASS_7.3-58 rappdirs_0.3.3 readr_2.1.3 cli_3.6.2
[106] parallel_4.2.2 dotCall64_1.1-1 igraph_1.6.0 pkgconfig_2.0.3 plotly_4.10.3
[111] spatstat.sparse_3.0-3 xml2_1.3.6 stringr_1.5.1 callr_3.7.3 digest_0.6.33
[116] RcppAnnoy_0.0.21 spatstat.data_3.0-3 leiden_0.4.3.1 uwot_0.1.16 curl_5.2.0
[121] shiny_1.8.0 lifecycle_1.0.4 nlme_3.1-160 jsonlite_1.8.8 viridisLite_0.4.2
[126] fansi_1.0.6 pillar_1.9.0 lattice_0.20-45 fastmap_1.1.1 httr_1.4.7
[131] pkgbuild_1.3.1 survival_3.4-0 glue_1.6.2 remotes_2.4.2 png_0.1-8
[136] bit_4.0.5 ggforce_0.4.1 class_7.3-20 stringi_1.8.3 profvis_0.3.7
[141] RcppHNSW_0.5.0 memoise_2.0.1 irlba_2.3.5.1 future.apply_1.10.0