Error while running bambu on single-cell long-read RNA-seq data

[MapleLin-Bio]

Hi there,

I tried to run Bambu on single-cell long-read RNA-seq data. However, I encountered this error:

Running Bambu-v3.9.0
--- Start generating read class files ---
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/
JYTL_mapped_BC_UG_n_sorted
Number of alignments/reads: 57169241
Finished creating junction list with splice motif in 1 mins.
before strand correction, annotated introns: 227099 (0.0677805286068816%)
after strand correction, annotated introns: 227155 (0.0677972425052343)
prediction accuracy (CV) (higher for splice donor than splice acceptor)
estimate: 2019.34659299313
pValue: 0
AUC: 0.996571317443796
prediction accuracy (CV) (higher for splice donor than splice acceptor)
estimate: 1231.23077052546
pValue: 0
AUC: 0.9924545777286
prediction accuracy (CV) (higher for splice donor than splice acceptor)
estimate: 1428.66432954738
pValue: 0
AUC: 0.993690816570014
prediction accuracy (CV) (higher for splice donor than splice acceptor)
estimate: 2270.15667946514
pValue: 0
AUC: 0.996101237546735
Model to predict true splice sites built in 0.3 mins.
reads count for all annotated junctions: 114108524 (0.953031493249955%)
reads count for all annotated junctions after correction to reference junction: 114292828 (0.954570795575274%)
Finished correcting junction based on set of high confidence junctions in 0.5 mins.
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in tibble(chr = as.factor(getChrFromGrList(readGrgList)), intronStarts = unname(unstrsplit(splitAsList(as.character(unlisted_junctions_start), : Tibble columns must have compatible sizes.
In addition: Warning messages:
1: In bambu.processReadsByFile(bam.file = reads[i], genomeSequence = genomeSequence,  :
  not all chromosomes present in reference annotations, annotations might be incomplete. Please compare objects on the same reference
2: In isore.constructReadClasses(readGrgList, unlisted_junctions, uniqueJunctions,  :
  read Id not sorted, can result in wrong assignments.
            Please report this
Execution halted

I have tried to keep main chromosomes (chr1–22/X/Y/M) or sort .bam file by readID, but the same error still occurs.
The code was:

se <- bambu(reads = sample_bam, annotations = ref_anno, genome = ref_fa, discovery = FALSE, quant = TRUE,
            demultiplexed = TRUE, verbose = TRUE, opt.em = list(degradationBias = FALSE), assignDist = TRUE, yieldSize = 10000000)

I wonder why this error occurs or how to resolve it?

Thank you in advance!