GetGRangesFromEnsDb: "The 2 combined objects have no sequence levels in common"

[f6v]

I'm analysing the paired RNA-seq and ATAC-seq data according to the [tutorial].(https://satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis.html) I get the "The 2 combined objects have no sequence levels in common" warning when running GetGRangesFromEnsDb(EnsDb.Hsapiens.v75).

Full log

> Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > Fetching data...OK > Parsing exons...OK > Defining introns...OK > Defining UTRs...OK > Defining CDS...OK > aggregating... > Done > The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.)The 2 combined objects have no sequence levels in common. (Use > suppressWarnings() to suppress this warning.) >

The code:

grange_counts <- StringToGRanges(rownames(atac_counts), sep = c("_", "_"))
grange_use <- seqnames(grange_counts) %in% standardChromosomes(grange_counts)
atac_counts <- atac_counts[as.vector(grange_use), ]
annotations <- GetGRangesFromEnsDb(EnsDb.Hsapiens.v75)
#seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "hg19"

chrom_assay <- CreateChromatinAssay(
   counts = atac_counts,
   sep = c("_", "_"),
   genome = 'hg19',
   annotation = annotations
 )

This is how the atac_counts looks like:

                   scCAT_HCT116_Batch1_1 scCAT_HCT116_Batch1_2 scCAT_HCT116_Batch1_3
chr1_10292_10791                       0                     0                     1
chr1_713838_714337                     1                     3                     2
chr1_762665_763164                     0                     5                     0

I don't quite understand what the consequences of this issue are. Any tips?

[f6v]

This probably isn't a bug, but I don't know how to change the label now.

[timoast]

Is there a reason you commented out the seqlevelsStyle step? It looks like your peaks are UCSC style, not Ensembl

[f6v]

@timoast the message pops up before seqlevelsStyle is invoked anyway. You're right that the peaks have different style, but it seems like Signac(or underlying library) can handle that? I've seen the same message as I was going through the vignette https://satijalab.org/signac/articles/mouse_brain_vignette.html I assume this warning isn't critical?

[timoast]

You're right that the peaks have different style, but it seems like Signac(or underlying library) can handle that?

No, the chromosome names need to match.

[meltager]

I was testing following the Motif analysis vignette (https://satijalab.org/signac/articles/mouse_brain_vignette.html), and i have build around it some code and it was working good till yesterday. Today, I start got error when running the following couple lines

annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Mmusculus.v79)
seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "mm10"

The error message i got is :

Error in .order_seqlevels(chrom_sizes[, "chrom"]) : 
  !anyNA(m31) is not TRUE 
17.
stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p))) 
16.
stopifnot(!anyNA(m31)) at mm10.R#24
15.
.order_seqlevels(chrom_sizes[, "chrom"]) at mm10.R#42
14.
GET_CHROM_SIZES(goldenPath.url = goldenPath.url) 
13.
.get_chrom_info_for_registered_UCSC_genome(script_path, assembled.molecules.only = assembled.molecules.only, 
    map.NCBI = map.NCBI, add.ensembl.col = add.ensembl.col, goldenPath.url = goldenPath.url, 
    recache = recache) 
12.
getChromInfoFromUCSC(new_genome, map.NCBI = TRUE) 
11.
(function (seqlevels, genome, new_style) 
{
    ans <- DataFrame(seqlevels = seqlevels, genome = genome)
    if (is.na(genome) || !(new_style %in% c("NCBI", "RefSeq",  ... 
10.
mapply(FUN = FUN, ..., MoreArgs = MoreArgs, SIMPLIFY = SIMPLIFY, 
    USE.NAMES = USE.NAMES) 
9.
eval(mc, env) 
8.
eval(mc, env) 
7.
eval(mc, env) 
6.
standardGeneric("mapply") 
5.
mapply(.set_seqlevelsStyle_from_seqlevels_and_genome, genome2seqlevels, 
    names(genome2seqlevels), MoreArgs = list(value), SIMPLIFY = FALSE, 
    USE.NAMES = FALSE) 
4.
`seqlevelsStyle<-`(`*tmp*`, value = value) 
3.
`seqlevelsStyle<-`(`*tmp*`, value = value) 
2.
`seqlevelsStyle<-`(`*tmp*`, value = "UCSC") 
1.
`seqlevelsStyle<-`(`*tmp*`, value = "UCSC") 

And here is part of my sessionInfo()

[1] EnsDb.Mmusculus.v79_2.99.0 ensembldb_2.14.1           AnnotationFilter_1.14.0    GenomicFeatures_1.42.3     AnnotationDbi_1.52.0      
 [6] Biobase_2.50.0             Signac_1.2.1               GenomicRanges_1.42.0       GenomeInfoDb_1.26.7        IRanges_2.24.1            
[11] S4Vectors_0.28.1           BiocGenerics_0.36.1       

[jardplard]

Was the original issue ever resolved here? I am also getting the same array of warning messages, and the GRanges object I receive is much larger than I would expect it to be.

[dy-lin]

For the error on seqlevelsStyle(), see: https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409252404 https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932