Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boundaries of non-circular sequence "chr2"
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Yue • 0
@c4d4e0fd
Last seen 8 weeks ago
Hong Kong

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
HiCDCPlus BSgenome.Hsapiens.UCSC.hg38 • 90 views
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