BiocParallel Error - Githubissues

I have been running bambu successfully on some files, but for other reasons I need to split these bam files by chromosome before analysis. After splitting, I've gotten the below error. Some of the chromosomes had low (single digit) reads, so I tried applying a filter so that only files with at least 1000 reads were pushed through to bambu. I still am getting the error. Any idea what the problem might be? There's no difference in the annotation or reference used that has been successful before, and the bam file has just been split by chromosome (before sorting and indexing). I've included the command used to run it and the traceback below.

Command: ` library(bambu)

 \# Run bambu isoform analysis
 isoforms <- bambu(reads = \'SMALL_TEST_T1_GL383522.1.bam\', annotations = \'/home/tylera/projects/abbvie/test_data     /gencode.gtf\',
         genome =\ '/home/tylera/projects/abbvie/test_data/GRCh38.p13.gencode.fa\')

Traceback:

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, 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: rtracklayer
If you are running bambu multiple times we recommend processing your annotation file first with annotations = prepareAnnotations(gtf.file)
--- Start generating read class files ---
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'i' in selecting a method for function '[': error in evaluating the argument 'table' in selecting a method for function '%in%': unable to find an inherited method for function ‘mcols’ for signature ‘"list"’
In addition: Warning messages:
1: In findHighConfidenceJunctions(junctions = uniqueJunctions, junctionModel = junctionModel,  :
  no junction correction as no high confidence reference junctions found
2: In max(start) : no non-missing arguments to max; returning -Inf
3: In min(end) : no non-missing arguments to min; returning Inf
Execution halted

GoekeLab / bambu

BiocParallel Error #341