ripSeek error : no method or default for coercing “NULL” to “GRanges”

Question

[maria]

Good afternoon,

I am trying to analyse RIP-seq data using the R library RIPseeker. Specifically, I am using the ripSeek() function, like so:

    runRipSeek <- function(bamPath) {
  #Set ripSeek parameters
  cNAME_input <- '_INPUT'
  biomaRt_dataset <- "hsapiens_gene_ensembl"
  goAnno <- "org.Hs.eg.db"
  outDir_input_as_controls <- "ripSeeker_out"
  biomart <- "ensembl"
  multicore <- TRUE
  print("Doing ripSeek command on:")
  print(bamPath)
  # Doing ripSeek command in parallel
  ripSeek_results_INPUT_controls <- ripSeek(
    bamPath = unname(bamPath),
    cNAME = cNAME_input,
    binSize = NULL,
    biomaRt_dataset = biomaRt_dataset,
    goAnno = goAnno,
    exportFormat = "bed",
    annotateFormat = "txt",
    annotateType = "TSS",
    outDir = outDir_input_as_controls,
    padjMethod = "BH",
    logOddCutoff = 1,
    pvalCutoff = 0.1,
    pvalAdjCutoff = 0.2,
    eFDRCutoff = 0.2,
    multicore = multicore,
    biomart = biomart,
    uniqueHit = TRUE,
    assignMultihits = TRUE,
    rerunWithDisambiguatedMultihits = TRUE,
    paired = TRUE,
    mc.cores = 20)
}

Everything is running smoothly until I get this error:

Error in FUN(X[[i]], ...) :
no method or default for coercing “NULL” to “GRanges”
Calls: runRipSeek -> ripSeek -> mainSeek -> GRangesList
In addition: Warning messages:
1: In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode,  :
    345176 alignments with ambiguous pairing were dumped.
    Use 'getDumpedAlignments()' to retrieve them from the dump environment.
2: In GenomicRanges:::valid.GenomicRanges.seqinfo(x) :
  GAlignments object contains 569964 out-of-bound ranges located on
  sequences chr1, chr2, chr3, chr4, chr5, chr6, chr9, chr10, chr12,
  chr13, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX,
  chrY, chrM, MU273366.1, ML143352.1, KQ759762.2, KQ031383.1, MU273333.1,
  KN538369.1, MU273382.1, ML143362.1, ML143365.1, MU273369.1, KN538360.1,
  KZ208920.1, KZ208906.1, KN196484.1, KZ208917.1, MU273343.1, KZ208911.1,
  KN196475.1, MU273348.1, KN538361.1, KN196474.1, ML143360.1, KZ559109.1,
  ML143359.1, MU273379.1, KN196480.1, ML143370.1, KQ090028.1, KN538363.1,
  KQ031385.1, KV766192.1, KN538370.1, KV880765.1, MU273362.1, MU273342.1,
  MU273374.1, KV766196.1, KN538371.1, MU273355.1, KQ090021.1, ML143371.1,
  MU273380.1, KZ208914.1, ML143373.1, ML143369.1, ML143366.1, ML143367.1,
  ML143372.1, ML143380.1, ML143377.1, MU273335.1, MU273392.1, ML143345.1,
  MU273373.1, MU273385.1, KQ458386.1, KV575244.1, MU273376.1, MU273377.1,
  MU273389.1, ML143354.1, ML143349.1, KZ208912.1, ML143 [... truncated]
3: In galp2gal(readGAlignmentPairs(alignFilePath, use.names = TRUE,  :
  573973 read-pairs with end larger than chromosome length are discarded
4: In mclapply(as.list(split(alignGR, seqnames(alignGR))), mainSeekSingleChrom,  :
  scheduled cores 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15 did not deliver results, all values of the jobs will be affected
Execution halted

I am not sure why this happens.. Reads were mapped to the latest version of the human genome assemby I dowloaded from the gencode website (human genome (GRCh38), version 44 (Ensembl 110)), using STAR v.2.7.0e. Thank you in advance for your help.