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Hi, I am doing the differential loop analysis by HiCDCPlus packages. However I encountered an issue during the construct_features
step. Here I paste the error. Could anyone give some adivce on what should I do during this situation? Many thanks!
construct_features(output_path=paste0(outdir,"/hg38_5kb_GATC"),
gen="Hsapiens",
gen_ver = 'hg38',
sig="GATC",bin_type="Bins-uniform",
binsize=5000,
chrs = c(paste0('chr', seq(1,22)), 'chrX', 'chrY'))
#the error went like this
> construct_features(output_path=paste0(outdir,"/hg38_5kb_GATC"),
+ gen="Hsapiens",
+ gen_ver = 'hg38',
+ sig="GATC",bin_type="Bins-uniform",
+ binsize=5000,
+ chrs = c(paste0('chr', seq(1,22)), 'chrX', 'chrY'))
Using chr1and cut patterns GATC
Joining, by = "bins"
Joining, by = "bins"
Joining, by = "bins"
Using chr2and cut patterns GATC
Error in loadFUN(x, seqname, ranges) :
trying to load regions beyond the boundaries of non-circular sequence "chr2"
此外: Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 2195 out-of-bound ranges located on sequence chr2. 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.
sessionInfo( )
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.4 BSgenome.Hsapiens.UCSC.hg19_1.4.3
[3] BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0_1.5.0 HiCDCPlus_1.6.0
[5] BSgenome_1.66.1 rtracklayer_1.58.0
[7] Biostrings_2.66.0 XVector_0.38.0
[9] DESeq2_1.38.1 SummarizedExperiment_1.28.0
[11] Biobase_2.58.0 MatrixGenerics_1.10.0
[13] matrixStats_0.63.0 GenomicRanges_1.50.1
[15] GenomeInfoDb_1.34.3 IRanges_2.32.0
[17] S4Vectors_0.36.0 BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] httr_1.4.4 tidyr_1.2.1 bit64_4.0.5 splines_4.2.2
[5] R.utils_2.12.2 assertthat_0.2.1 BiocManager_1.30.19 blob_1.2.3
[9] GenomeInfoDbData_1.2.9 Rsamtools_2.14.0 yaml_2.3.6 pillar_1.8.1
[13] RSQLite_2.2.18 lattice_0.20-45 glue_1.6.2 RColorBrewer_1.1-3
[17] colorspace_2.0-3 R.oo_1.25.0 Matrix_1.5-1 XML_3.99-0.12
[21] pkgconfig_2.0.3 zlibbioc_1.44.0 purrr_0.3.5 xtable_1.8-4
[25] scales_1.2.1 BiocParallel_1.32.3 tibble_3.1.8 annotate_1.76.0
[29] KEGGREST_1.38.0 generics_0.1.3 ggplot2_3.4.0 ellipsis_0.3.2
[33] withr_2.5.0 cachem_1.0.6 cli_3.4.1 magrittr_2.0.3
[37] crayon_1.5.2 memoise_2.0.1 R.methodsS3_1.8.2 fansi_1.0.3
[41] tools_4.2.2 data.table_1.14.6 BiocIO_1.8.0 lifecycle_1.0.3
[45] munsell_0.5.0 locfit_1.5-9.6 DelayedArray_0.24.0 AnnotationDbi_1.60.0
[49] compiler_4.2.2 rlang_1.0.6 grid_4.2.2 RCurl_1.98-1.9
[53] rstudioapi_0.14 rjson_0.2.21 rappdirs_0.3.3 bitops_1.0-7
[57] restfulr_0.0.15 gtable_0.3.1 codetools_0.2-18 DBI_1.1.3
[61] R6_2.5.1 GenomicAlignments_1.34.0 dplyr_1.0.10 fastmap_1.1.0
[65] bit_4.0.5 utf8_1.2.2 parallel_4.2.2 Rcpp_1.0.9
[69] vctrs_0.5.1 geneplotter_1.76.0 png_0.1-7 tidyselect_1.2.0
I guess you are mixing the NCBI and UCSC annotations. If you are using a custom-edited code to load the annotations, I would recommend cloning a copy from this repo, change the ".UCSC" coding in the following files to ".NCBI"