Hello, how long does it take to process spatial transcriptome data with bambu-singlecell-spatial?

[xyz202310]

Hi,
Thank you for developing this tool! I want to know how long it takes to process spatial transcriptome data with bambu-singlecell-spatial. I am using the spatial transcriptome data provided in the paper; it has already been running for 1 day and 20 hours and has not finished yet—is this normal? I have one more request: could you please upload the high-resolution histological images corresponding to the spatial transcriptome data in the Bambu-Clump paper? Thank you very much!
Amanda

[xyz202310]

Hello, I ran the test files from the example and encountered the following error during the bambu_EM step:

Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in (function (cond) : error in evaluating the argument 'obj' in selecting a method for function 'unname': object of type 'S4' is not subsettable
Execution halted

The complete output file is attached.

outfile.txt

[lingminhao]

Hi @xyz202310 ,

Sorry for the late reply.

We encountered this bug and have attempted to fix this in the revision branch of this repository. Can you try to rerun the pipeline on test files with the revision branch?

Best Regards,
Min Hao

[xyz202310]

Hi, @lingminhao ,
Thanks for your reply. I'm trying it.
I have one more request: could you please upload the high-resolution histological images corresponding to the spatial transcriptome data in the Bambu-Clump paper ( Figure 5 (a) A digital photo of the mouse brain sample on the 10x slide ) ? Thank you!

[xyz202310]

Hi, @lingminhao,
I tried the revision branch, but it still fails at the bambu_EM step:
Command executed:

#!/usr/bin/env Rscript
#.libPaths("/usr/local/lib/R/site-library")
library(devtools)
if("bambu" == "bambu") {
load_all("/mnt/software/bambu")
} else {
load_all("bambu")
}
if(".txt" %in% "combined"){runName = readLines("combined")
} else{runName = "combined"}

 extendedAnno <- readRDS("Bambu_extended_annotations.rds")
 quantDatas = readRDS("Bambu_quantData.rds")
 clusters = readRDS("Bambu_clusters.rds")

print(clusters)
degBias = TRUE
if(is.null(clusters)){degBias = FALSE}
se = bambu( reads = "Bambu_readClassFile.rds",
annotations = extendedAnno,
genome = "Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa",
quantData = quantDatas,
assignDist = FALSE,
ncore = 16,
discovery = FALSE,
quant = TRUE,
demultiplexed = TRUE,
verbose = FALSE,
opt.em = list(degradationBias = degBias),
clusters = clusters)
saveRDS(se, paste0(runName, "_se.rds"))
writeBambuOutput(se, path = ".", prefix = paste0(runName, "EM"),outputExtendedAnno = FALSE,
outputAll = FALSE, outputBambuModels = FALSE, outputNovelOnly = FALSE)

Command exit status:
1

Command output:
[[1]]
CharacterList of length 2
[["Bambu_0"]] Bambu_AACGTTGAGAGTAAGG ... Bambu_TTGCGTCCAGTAGAGC
[["Bambu_1"]] Bambu_AAACGGGGTGCGATAG ... Bambu_TTGACTTAGCTGCAAG

Command error:
Welcome to Bioconductor

  Vignettes contain introductory material; view with
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

  rowMedians

The following objects are masked from 'package:matrixStats':

  anyMissing, rowMedians

Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

  strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

  FileForFormat

[[1]]
CharacterList of length 2
[["Bambu_0"]] Bambu_AACGTTGAGAGTAAGG ... Bambu_TTGCGTCCAGTAGAGC
[["Bambu_1"]] Bambu_AAACGGGGTGCGATAG ... Bambu_TTGACTTAGCTGCAAG

Running Bambu-v3.9.0
WARNING - If you change the number of cores (ncore) between Bambu runs and there is no progress please restart your R session to resolve the issue that originates from the XGboost package.
--- Start isoform EM quantification ---
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in (function (cond) : error in evaluating the argument 'obj' in selecting a method for function 'unname': object of type 'S4' is not subsettable
Execution halted