Warning message when using AddMotifs

Hello, since using ouput from the GRCh38 reference build for cellranger-atac 2.0.0 (refdata-cellranger-arc-GRCh38-2020-A-2.0.0), I am having issues related to scaffold annotation specifically during the "Creating Motif object" stage of the AddMotifs code block. You'll see at the end of the code that I've tried to remove scaffold peaks as you described #486, and this allows the AddMotifs function to run past the Building Motif matrix block before throwing up the error I show at the bottom ... have I missed an easy step during annotation here? Thanks in advance for any help.

Minimum reproducible code assuming merge vignette:

library(Seurat)
library(Signac)
library(GenomeInfoDb)
library(EnsDb.Hsapiens.v86)
library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg38)
library(JASPAR2020)
library(motifmatchr)
library(TFBSTools)
library(ggplot2)
library(patchwork)
set.seed(1234)

peaks1 <- read.table(
  file = "sample1/peaks.bed",
  col.names = c("chr", "start", "end")
)

peaks2 <- read.table(
  file = "sample2/peaks.bed",
  col.names = c("chr", "start", "end")
)

gr.1 <- makeGRangesFromDataFrame(peaks1)
gr.2 <- makeGRangesFromDataFrame(peaks2)

combined.peaks <- reduce(x = c(peaks1, peaks2))

peakwidths <- width(combined.peaks)
combined.peaks <- combined.peaks[peakwidths  < 10000 & peakwidths > 20]
combined.peaks

md.1 <- read.table(
  file = "/sample1/singlecell.csv",
  stringsAsFactors = FALSE,
  sep = ",",
  header = TRUE,
  row.names = 1
)[-1, ]

md.2 <- read.table(
  file = "/sample2/singlecell.csv",
  stringsAsFactors = FALSE,
  sep = ",",
  header = TRUE,
  row.names = 1
)[-1, ]

md.1 <- md.1[md.1$passed_filters > 500, ]
md.2 <- md.2[md.2$passed_filters > 500, ]

frags.1 <- CreateFragmentObject(
  path = "/sample1/fragments.tsv.gz",
  cells = rownames(md.1)
)

frags.2 <- CreateFragmentObject(
  path = "/sample1/fragments.tsv.gz",
  cells = rownames(md.2)
)

counts.1 <- FeatureMatrix(
  fragments = frags.1,
  features = combined.peaks,
  cells = rownames(md.1)
)

counts.2 <- FeatureMatrix(
  fragments = frags.2,
  features = combined.peaks,
  cells = rownames(md.2)
)

sample1_assay <- CreateChromatinAssay(counts.1, fragments = frags.1)
sample1_ATAC <- CreateSeuratObject(sample1_assay, assay = "ATAC", meta.data = md.1, project = "sample1")

sample2_assay <- CreateChromatinAssay(counts.2, fragments = frags.2)
sample2_ATAC <- CreateSeuratObject(sample2_assay, assay = "ATAC", meta.data = md.2, project = "sample2")

sample1_ATAC$sample <- 'sample1'
sample2_ATAC$sample <- 'sample2'

combined <- merge(x=sample1_ATAC,
                  y=sample2_ATAC,
                  add.cell.ids=c("s1","s2"))

combined <- RunTFIDF(combined)
combined <- FindTopFeatures(combined, min.cutoff = 20)
combined <- RunSVD(combined)
combined <- RunUMAP(combined, dims = 2:50, reduction = 'lsi')

annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "hg38"
Annotation(combined) <- annotations

main.chroms <- standardChromosomes(BSgenome.Hsapiens.UCSC.hg38)
keep.peaks <- as.logical(seqnames(granges(combined)) %in% main.chroms)
combined <- combined[keep.peaks, ]

pfm <- getMatrixSet(x = JASPAR2020,opts = list(species = 9606, all_versions = FALSE))
combined <- AddMotifs(combined, genome=BSgenome.Hsapiens.UCSC.hg38, pfm=pfm)

Error:

Building motif matrix
Finding motif positions
Creating Motif object
Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270772v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr4_GL000 [... truncated]
2: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270772v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr4_GL000 [... truncated]
3: In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270772v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr4_GL000 [... truncated]

stuart-lab / signac

Warning message when using AddMotifs #729