createArrowFiles: ERROR Found in .addGeneScoreMat

[tao-bioinfo]

ArrowFiles = createArrowFiles(inputFiles = c("test.tsv.gz"), sampleNames = c("test"), minTSS=2.5, addTileMat = TRUE, addGeneScoreMat = TRUE, geneAnnotation=geneAnnotation, genomeAnnotation=genomeAnnotation)

It results in:

ERROR Found in .addGeneScoreMat for (test : 1 of 1) 
LogFile = ArchRLogs/ArchR-createArrows-b87e4ba93b76-Date-2021-07-17_Time-10-27-19.log

<simpleError in (function (classes, fdef, mtable) {    methods <- .findInheritedMethods(classes, fdef, mtable)    if (length(methods) == 1L)         return(methods[[1L]])    else if (length(methods) == 0L) {        cnames <- paste0("\"", vapply(classes, as.character,             ""), "\"", collapse = ", ")        stop(gettextf("unable to find an inherited method for function %s for signature %s",             sQuote(fdef@generic), sQuote(cnames)), domain = NA)    }    else stop("Internal error in finding inherited methods; didn't return a unique method",         domain = NA)})(list("NULL"), new("standardGeneric", .Data = function (x) standardGeneric("seqnames"), generic = structure("seqnames", package = "GenomeInfoDb"),     package = "GenomeInfoDb", group = list(), valueClass = character(0),     signature = "x", default = NULL, skeleton = (function (x)     stop("invalid call in method dispatch to 'seqnames' (no default method)",         domain = NA))(x)), <environment>): unable to find an inherited method for function ‘seqnames’ for signature ‘"NULL"’>

If I set addGeneScoreMat = FALSE, then it's OK.

However I guarantee gene information has been contained in geneAnnotation :

> geneAnnotation$genes
GRanges object with 69008 ranges and 1 metadata column:
          seqnames            ranges strand |                  seq_id
             <Rle>         <IRanges>  <Rle> |                <factor>
      [1]      A01       13133-15594      - |   Ghir_A01G000010_trm61
      [2]      A01       23150-23356      + |         Ghir_A01G000020
      [3]      A01       65234-68191      + |         Ghir_A01G000030
      [4]      A01       70861-74152      - | Ghir_A01G000040_Zcchc12
      [5]      A01       76841-77944      - |    Ghir_A01G000050_cmc2
      ...      ...               ...    ... .                     ...
  [69004]      D13 63270786-63274742      + |    Ghir_D13G025640_WNK4
  [69005]      D13 63286647-63287959      - |    Ghir_D13G025650_OFP3
  [69006]      D13 63294532-63297545      - | Ghir_D13G025660_tmem87a
  [69007]      D13 63300635-63303762      + |   Ghir_D13G025670_Slx1b
  [69008]      D13 63310090-63311548      + |         Ghir_D13G025680
  -------
  seqinfo: 26 sequences from an unspecified genome; no seqlengths

ArchR-createArrows-b87e4ba93b76-Date-2021-07-17_Time-10-27-19.log

[rcorces]

and you've run addArchRChrPrefix(chrPrefix = FALSE) as indicated in the manual?
If so, could be related to genes that are really close to chromosome ends or chromosomes with no reads. There have been some previous issues related to those edge cases. check the previous issues.

[tao-bioinfo]

Yes, I've run addArchRChrPrefix(chrPrefix = FALSE)

Could you be glad to put the URL links of related previous issues?

[tao-bioinfo]

Well, after adding a symbol column in my geneAnnotation, it has been fixed.

#792