Error using createGenomeAnnotation and createArrowFiles

[criveralopez]

I work with a non-model organism, Hofstenia miamia, and I am trying to create an arrow file. I am getting an error I think it is not allowing me to properly generate an arrow file because of the absence of information in the genomeAnnotation object. See below the error I get when I try to create the arrow file:

ArrowFiles <- createArrowFiles(
+     inputFiles = inputFiles,
+     sampleNames = c("homeostasisA", "homeostasisB"),
+     geneAnnotation = geneAnnotation,
+     genomeAnnotation = genomeAnnotation,
+     minTSS = 4,
+     minFrags = 1000,
+     maxFrags = 1e+05,
+     addTileMat = TRUE,
+     addGeneScoreMat = TRUE
+     )
Found Gene Seqnames not in GenomeAnnotation chromSizes, Removing : scaffold1,scaffold2,scaffold3,scaffold4,scaffold5,scaffold6,scaffold7,scaffold8
Found Exon Seqnames not in GenomeAnnotation chromSizes, Removing : scaffold1,scaffold2,scaffold3,scaffold4,scaffold5,scaffold6,scaffold7,scaffold8
Found TSS Seqnames not in GenomeAnnotation chromSizes, Removing : scaffold1,scaffold2,scaffold3,scaffold4,scaffold5,scaffold6,scaffold7,scaffold8
ArchR logging to : ArchRLogs/ArchR-createArrows-50fdec6000e-Date-2023-04-27_Time-14-07-25.log
If there is an issue, please report to github with logFile!
2023-04-27 14:07:26 : Batch Execution w/ safelapply!, 0 mins elapsed.
2023-04-27 14:07:26 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
ArchR logging successful to : ArchRLogs/ArchR-createArrows-50fdec6000e-Date-2023-04-27_Time-14-07-25.log
Warning message:
In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) :
  2 function calls resulted in an error

The BSgenome seems to have all the information, at least from my understanding, see below:

> BSgenome.Hmiamia.Harvard.Hm2
Three banded panther worm genome:
# organism: Hofstenia miamia (Three banded panther worm)
# genome: Hm2
# provider: Harvard
# release date: Unreleased
# 8 sequences:
#   scaffold1 scaffold2 scaffold3 scaffold4 scaffold5 scaffold6
#   scaffold7 scaffold8                                        
# (use 'seqnames()' to see all the sequence names, use the '$'
# or '[[' operator to access a given sequence)
> seqinfo(BSgenome.Hmiamia.Harvard.Hm2)
Seqinfo object with 8 sequences from Hm2 genome:
  seqnames  seqlengths isCircular genome
  scaffold1  138991948      FALSE    Hm2
  scaffold2  137431522      FALSE    Hm2
  scaffold3  124383454      FALSE    Hm2
  scaffold4  122288621      FALSE    Hm2
  scaffold5  113097833      FALSE    Hm2
  scaffold6  106762072      FALSE    Hm2
  scaffold7   99744246      FALSE    Hm2
  scaffold8   94572010      FALSE    Hm2

However, when I try creating the genome Annotation as shown below, I believe it is not transferring the information properly to the genomeAnnotation object:

genomeAnnotation <- createGenomeAnnotation(genome = BSgenome.Hmiamia.Harvard.Hm2)
> genomeAnnotation
List of length 3
names(3): genome chromSizes blacklist
> seqinfo(genomeAnnotation)
Seqinfo object with 3 sequences from an unspecified genome; no seqlengths:
  seqnames   seqlengths isCircular genome
  genome             NA         NA   <NA>
  chromSizes         NA         NA   <NA>
  blacklist          NA         NA   <NA>

Maybe perhaps this is the main issue with the arrow file... Any thoughts? Thanks in advance!

[HaixJiang]

Have you solved your problem? Can you share it with me?