bambuEM error: object of type 'S4' is not subsettable #14
Description
Thanks for providing single-cell version of bambu, ..however I am getting an error in the EM step, just running the example. I ran from the directory where nextflow was installed, based on comments in a previous issue. Command and full sysout pasted below:
nextflow run main.nf --bams $BAMBU_DIR/examples/demultiplexed.bam --genome $BAMBU_DIR/examples/Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa --annotation $BAMBU_DIR/examples/Homo_sapiens.GRCh38.91_chr9_1_1000000.gtf --ncore 16 --outdir output -with-singularity lingminhao/bambusc:beta1.2
N E X T F L O W ~ version 25.04.3
Launching main.nf [naughty_visvesvaraya] DSL2 - revision: 5dc06a459c
executor > local (2)
[9a/4c02dd] bambu | 1 of 1 ?
[99/a4aef8] bambu_EM | 0 of 1
ERROR ~ Error executing process > 'bambu_EM'
Caused by:
Process bambu_EM terminated with an error exit status (1)
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")
degBias = TRUE
if(is.null(clusters)){degBias = FALSE}
se = bambu( reads = "test.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:
(empty)
Command error:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
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':
executor > local (2)
[9a/4c02dd] bambu | 1 of 1 ?
[99/a4aef8] bambu_EM | 0 of 1 ?
ERROR ~ Error executing process > 'bambu_EM'
Caused by:
Process bambu_EM terminated with an error exit status (1)
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")
degBias = TRUE
if(is.null(clusters)){degBias = FALSE}
se = bambu( reads = "test.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:
(empty)
Command error:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
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
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
Work dir:
/home/sgrimes/.nextflow/assets/GoekeLab/bambu-singlecell-spatial/work/99/a4aef8e8f523d0100314a99b0aff6a
Container:
/home/sgrimes/.nextflow/assets/GoekeLab/bambu-singlecell-spatial/work/singularity/lingminhao-bambusc-beta1.2.img
Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
-- Check '.nextflow.log' file for details