merge muti atac data error:obj.combined <- merge(obj.list[[1]],obj.list[2:4])

[Zhaowado]

when I follow the Vignettes (scATAC-seq data integration) to merge muti atac data, I've successfully created four objects via CreateChromatinAssay and CreateSeuratObject. However, when I merge the four objects, i got the error: Error in .get_data_frame_col_as_numeric(df, granges_cols[["start"]]) :
some values in the "start" column cannot be turned into numeric values
In addition: Warning message:
Expected 3 pieces. Additional pieces discarded in 53858 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

Here is my code:
`library(Signac)
library(Seurat)
library(ggplot2)
library(Matrix)

obj.list <- list()
sample.list <- c("sexual_0h","sexual_5d","sexual_7d","sexual_WT")
frag.path <- "/dellfsqd2/ST_LBI/USER/****/projects/wochong/11.atac/00.frag_data"
for (i in sample.list) {
counts <- readMM(paste0(frag.path,"/",i,".Peak_matrix/matrix.mtx"))
barcodes <- read.table(paste0(frag.path,"/",i,".Peak_matrix/barcodes.tsv"))
peaks <- read.table(paste0(frag.path,"/",i,".Peak_matrix/peak.bed"))
rownames(counts) <- peaks$V1
colnames(counts) <- barcodes$V1
metadata <- read.csv(paste0("/dellfsqd2/ST_OCEAN/USER/*****/Project/10.smed.sexual/06.scATAC/01.QC/",i,"/output/",i,".Metadata.tsv"),
sep = "\t",row.names = 1)
metadata$Sample <- i
chrom_assay <- CreateChromatinAssay(
counts = counts,
sep = c(":", "-","_"),
fragments = paste0(frag.path,"/",i,".fragments.tsv.gz"),
min.cells = 10,
min.features = 200
)
obj.list[[i]] <- CreateSeuratObject(
counts = chrom_assay,
assay = "peaks",
meta.data = metadata
)
obj.list[[i]] <- FindTopFeatures(obj.list[[i]], min.cutoff = 10)
obj.list[[i]] <- RunTFIDF(obj.list[[i]])
obj.list[[i]] <- RunSVD(obj.list[[i]])
}
obj.combined <- merge(obj.list[[1]],obj.list[2:4]) `

Hope to get reply 🙏🙏🙏

[timoast]

Please open an issue and include the output of sessionInfo()

[Zhaowado]

Thanks for your reply. I've solved this problem. This error is reported may because my rownames (counts) are separated by '', similar to dd_Smes_g4_99-2151278-2151524. When I run CreateChromatinAssay(), I find a warning:
Warning: Feature names cannot have underscores (''), replacing with dashes ('-').
This resulted in the features in chrom_assay become dd-Smes-g4-99-2151278-2151524, however, when merge these object, I guess you may use '-' to separate characters by default. This caused this error to occur.

Then I change my chr scaffold name into dd.Smes.g4.x, this error is solved.
Now I wander can this warning be avoided?

Here is the output of sessionInfo()：

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /dellfsqd2/ST_LBI/USER/*/Tools/anaconda3_new/anaconda3_new/envs/signsc/lib/libopenblasp-r0.3.26.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: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
[1] Matrix_1.6-5 ggplot2_3.5.0 SeuratObject_5.0.1 Seurat_4.3.0.1
[5] Signac_1.12.0

loaded via a namespace (and not attached):
[1] bitops_1.0-7 deldir_2.0-2 pbapply_1.7-2
[4] gridExtra_2.3 rlang_1.1.3 magrittr_2.0.3
[7] RcppAnnoy_0.0.22 spatstat.geom_3.2-8 matrixStats_1.2.0
[10] ggridges_0.5.6 compiler_4.3.2 reshape2_1.4.4
[13] png_0.1-8 vctrs_0.6.5 stringr_1.5.1
[16] pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.1.1
[19] XVector_0.42.0 ellipsis_0.3.2 utf8_1.2.4
[22] Rsamtools_2.18.0 promises_1.2.1 purrr_1.0.2
[25] zlibbioc_1.48.0 GenomeInfoDb_1.38.6 jsonlite_1.8.8
[28] goftest_1.2-3 later_1.3.2 spatstat.utils_3.0-4
[31] BiocParallel_1.36.0 irlba_2.3.5.1 parallel_4.3.2
[34] cluster_2.1.6 R6_2.5.1 ica_1.0-3
[37] spatstat.data_3.0-4 stringi_1.8.3 RColorBrewer_1.1-3
[40] reticulate_1.35.0 parallelly_1.37.0 scattermore_1.2
[43] lmtest_0.9-40 GenomicRanges_1.54.1 Rcpp_1.0.12
[46] RcppRoll_0.3.0 tensor_1.5 future.apply_1.11.1
[49] zoo_1.8-12 sctransform_0.4.1 IRanges_2.36.0
[52] httpuv_1.6.14 splines_4.3.2 igraph_2.0.2
[55] tidyselect_1.2.0 abind_1.4-5 spatstat.random_3.2-2
[58] spatstat.explore_3.2-6 codetools_0.2-19 miniUI_0.1.1.1
[61] listenv_0.9.1 plyr_1.8.9 lattice_0.22-5
[64] tibble_3.2.1 withr_3.0.0 shiny_1.8.0
[67] ROCR_1.0-11 Rtsne_0.17 future_1.33.1
[70] survival_3.5-8 polyclip_1.10-6 fitdistrplus_1.1-11
[73] Biostrings_2.70.2 pillar_1.9.0 KernSmooth_2.23-22
[76] stats4_4.3.2 plotly_4.10.4 generics_0.1.3
[79] sp_2.1-3 RCurl_1.98-1.14 S4Vectors_0.40.2
[82] munsell_0.5.0 scales_1.3.0 globals_0.16.2
[85] xtable_1.8-4 glue_1.7.0 lazyeval_0.2.2
[88] tools_4.3.2 data.table_1.14.10 RANN_2.6.1
[91] leiden_0.4.3.1 dotCall64_1.1-1 fastmatch_1.1-4
[94] cowplot_1.1.3 grid_4.3.2 tidyr_1.3.1
[97] colorspace_2.1-0 nlme_3.1-164 GenomeInfoDbData_1.2.11
[100] patchwork_1.2.0 cli_3.6.2 spatstat.sparse_3.0-3
[103] spam_2.10-0 fansi_1.0.6 viridisLite_0.4.2
[106] dplyr_1.1.4 uwot_0.1.16 gtable_0.3.4
[109] digest_0.6.34 progressr_0.14.0 BiocGenerics_0.48.1
[112] ggrepel_0.9.5 htmlwidgets_1.6.4 htmltools_0.5.7
[115] lifecycle_1.0.4 httr_1.4.7 mime_0.12
[118] MASS_7.3-60