Error in getFootprints

[sloanlewis]

Hi,

I am using archR for 10X scATAC-Seq data from rhesus macaque. I am trying to perform the footprinting analysis and am getting this error:
seFoot <- getFootprints(

• ArchRProj = proj,
• positions = motifPositions[markerMotifs],
• groupBy = "Clusters_celltype"
• )
  ArchR logging to : ArchRLogs/ArchR-getFootprints-a19b3da8e6cc-Date-2022-03-01_Time-20-11-03.log
  If there is an issue, please report to github with logFile!
  2022-03-01 20:11:07 : Computing Kmer Bias Table, 0.054 mins elapsed.
  Error in loadFUN(x, seqname, ranges) :
  trying to load regions beyond the boundaries of non-circular sequence "chrX"
  In addition: Warning message:
  In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence chrX. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?trim,GenomicRanges-method for more
  information.

I believe it's an error with my annotation file, but I can't figure it out. Any help is appreciated!

sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid parallel stats4 stats graphics utils datasets grDevices methods base

other attached packages:
[1] ComplexHeatmap_2.4.3 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.5 purrr_0.3.4
[6] readr_1.4.0 tidyr_1.1.3 tibble_3.1.1 tidyverse_1.3.1 ggrastr_0.2.3
[11] Cairo_1.5-12.2 ensembldb_2.12.1 AnnotationFilter_1.12.0 GenomicFeatures_1.40.1 org.Mmu.eg.db_3.11.4
[16] AnnotationDbi_1.50.3 BSgenome.Mmulatta.UCSC.rheMac8_1.4.2 BSgenome_1.56.0 rtracklayer_1.48.0 Biostrings_2.56.0
[21] XVector_0.28.0 ArchR_1.0.1 magrittr_2.0.1 rhdf5_2.32.4 Matrix_1.3-4
[26] data.table_1.14.0 SummarizedExperiment_1.18.2 DelayedArray_0.14.1 matrixStats_0.58.0 Biobase_2.48.0
[31] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1 BiocGenerics_0.34.0
[36] ggplot2_3.3.3 colorout_1.2-2

loaded via a namespace (and not attached):
[1] ggbeeswarm_0.6.0 colorspace_2.0-0 rjson_0.2.20 ellipsis_0.3.1 circlize_0.4.12 GlobalOptions_0.1.2 fs_1.5.0 clue_0.3-59
[9] rstudioapi_0.13 bit64_4.0.5 fansi_0.4.2 lubridate_1.7.10 xml2_1.3.2 cachem_1.0.4 jsonlite_1.7.2 Rsamtools_2.4.0
[17] broom_0.7.6 cluster_2.1.2 dbplyr_2.1.1 png_0.1-7 compiler_4.0.1 httr_1.4.2 backports_1.2.1 assertthat_0.2.1
[25] fastmap_1.1.0 lazyeval_0.2.2 cli_2.5.0 prettyunits_1.1.1 tools_4.0.1 gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.3
[33] rappdirs_0.3.3 Rcpp_1.0.7 cellranger_1.1.0 vctrs_0.3.6 ps_1.6.0 rvest_1.0.0 lifecycle_1.0.0 XML_3.99-0.6
[41] zlibbioc_1.34.0 scales_1.1.1 hms_1.0.0 ProtGenerics_1.20.0 RColorBrewer_1.1-2 curl_4.3 memoise_2.0.0 biomaRt_2.44.4
[49] stringi_1.5.3 RSQLite_2.2.7 BiocParallel_1.22.0 shape_1.4.5 rlang_0.4.10 pkgconfig_2.0.3 bitops_1.0-7 lattice_0.20-41
[57] Rhdf5lib_1.10.1 GenomicAlignments_1.24.0 bit_4.0.4 tidyselect_1.1.0 R6_2.5.0 generics_0.1.0 DBI_1.1.1 pillar_1.6.0
[65] haven_2.4.1 withr_2.4.2 RCurl_1.98-1.3 modelr_0.1.8 crayon_1.4.1 utf8_1.2.1 BiocFileCache_1.12.1 GetoptLong_1.0.5
[73] progress_1.2.2 readxl_1.3.1 blob_1.2.1 reprex_2.0.0 openssl_1.4.3 munsell_0.5.0 beeswarm_0.3.1 vipor_0.4.5
[81] askpass_1.1

ArchR-getFootprints-a19b3da8e6cc-Date-2022-03-01_Time-20-11-03.log

[rcorces]

Non-standard genomes are not something that we have experience working with. There have been many issues with this but they are challenging for us to diagnose given the variety of problems. I dont believe we've seen this issue before

[sloanlewis]

No problem. Is there something you can suggest for me to try to troubleshoot? I was thinking to subset out chrX from the GRanges object to see if that is the issue.

[rcorces]

My assumption would be that the footprinting is using a region very close to the ends of the chromosome and when it tries to extend the window to capture the surrounding signal it falls off the edge of the chromosome.

[woshiyangsi]

I have encountered the same problem, trying to load regions beyond the boundaries of non-circular sequence "chr8"
Have you solved it？

[Melody-cell]

@woshiyangsi ,hi,
i have encountered the sam problem, have you solved it ？