unable to forge custom BSgenome after update
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Chris Seidel ▴ 80
@chris-seidel-5840
Last seen 6 days ago
United States

I'm unable forge a custom genome with R 4.0.3 and BSgenome_1.58.0. I've successfully forged many custom genomes over the years, and I'm very confused about the error message.

forgeBSgenomeDataPkg("cws_analysis/BSGenome_NC_035897/BSgenome.Amexicanus.SIMR.astMexNC2-seed")
Error in .make_Seqinfo_from_genome(genome) : 
  "astMexNC" is not a registered NCBI assembly or UCSC genome (use
  registered_NCBI_assemblies() or registered_UCSC_genomes() to list the NCBI or
  UCSC assemblies/genomes currently registered in the GenomeInfoDb package)

Here is the seed file:

Package: BSgenome.Amexicanus.SIMR.astMexNC
Title: Astyanax mexicanus (Cave Fish) first chromosome (NCBI version surface)
Description: Washington University School of Medicine chromosome-level assembly of Astyanax_Mexicanus-2.0.
Version: 1.4.2
organism: Astyanax mexicanus
common_name: Cavefish
provider: SIMR
genome: astMex2NC
release_date: April 2017
release_name: Surface chr1 sequence
source_url: https://webfs/cws_analysis/BSGenome_NC_035897
organism_biocview: Astyanax_mexicanus
BSgenomeObjname: Amexicanus
SrcDataFiles: NC_035897.fa from https://webfs/cws_analysis/BSGenome_NC_035897/
PkgExamples: genome$NC_035897.1  # same as genome[["NC_035897.1"]]
seqs_srcdir: /home/cws/jak11/cws_analysis/BSGenome_NC_035897
seqfile_name: NC_035897.2bit

I don't understand why I'm getting an error about registered assemblies. I can successfully forge this genome using R4.0.0 and BSgenome_1.56.0, by simply swapping out "genome: astMexNC" for "provider_version: astMex2NC" in the seed file, as I understand provider_version is now deprecated in favor of genome. But the seed file above fails with BSgenome_1.58.0.

What am I doing wrong? Why is it looking for registered assemblies?

 > sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /n/apps/CentOS7/install/r-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /n/apps/CentOS7/install/r-4.0.3/lib64/R/lib/libRlapack.so

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

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

other attached packages:
 [1] BSgenome_1.58.0      motifbreakR_2.4.0    MotifDb_1.32.0       Biostrings_2.58.0   
 [5] XVector_0.30.0       rtracklayer_1.50.0   GenomicRanges_1.42.0 GenomeInfoDb_1.26.4 
 [9] IRanges_2.24.1       S4Vectors_0.28.1     BiocGenerics_0.36.0  pheatmap_1.0.12     
[13] knitr_1.31           RColorBrewer_1.1-2  

loaded via a namespace (and not attached):
  [1] colorspace_2.0-0            ellipsis_0.3.1              biovizBase_1.38.0          
  [4] htmlTable_2.1.0             base64enc_0.1-3             dichromat_2.0-0            
  [7] rstudioapi_0.13             bit64_4.0.5                 AnnotationDbi_1.52.0       
 [10] fansi_0.4.2                 xml2_1.3.2                  splines_4.0.0              
 [13] motifStack_1.34.0           cachem_1.0.4                ade4_1.7-16                
 [16] Formula_1.2-4               splitstackshape_1.4.8       Rsamtools_2.6.0            
 [19] cluster_2.1.1               dbplyr_2.1.0                png_0.1-7                  
 [22] compiler_4.0.0              httr_1.4.2                  backports_1.2.1            
 [25] assertthat_0.2.1            Matrix_1.3-2                fastmap_1.1.0              
 [28] lazyeval_0.2.2              htmltools_0.5.1.1           prettyunits_1.1.1          
 [31] tools_4.0.0                 TFMPvalue_0.0.8             gtable_0.3.0               
 [34] glue_1.4.2                  GenomeInfoDbData_1.2.4      dplyr_1.0.5                
 [37] rappdirs_0.3.3              Rcpp_1.0.6                  Biobase_2.50.0             
 [40] vctrs_0.3.6                 debugme_1.1.0               xfun_0.22                  
 [43] stringr_1.4.0               lifecycle_1.0.0             ensembldb_2.14.0           
 [46] XML_3.99-0.6                zlibbioc_1.36.0             MASS_7.3-53.1              
 [49] scales_1.1.1                VariantAnnotation_1.36.0    ProtGenerics_1.22.0        
 [52] hms_1.0.0                   MatrixGenerics_1.2.1        SummarizedExperiment_1.20.0
 [55] AnnotationFilter_1.14.0     yaml_2.2.1                  curl_4.3                   
 [58] memoise_2.0.0               gridExtra_2.3               ggplot2_3.3.3              
 [61] biomaRt_2.46.3              rpart_4.1-15                latticeExtra_0.6-29        
 [64] stringi_1.5.3               RSQLite_2.2.4               checkmate_2.0.0            
 [67] GenomicFeatures_1.42.2      BiocParallel_1.24.1         rlang_0.4.10               
 [70] pkgconfig_2.0.3             matrixStats_0.58.0          bitops_1.0-6               
 [73] evaluate_0.14               lattice_0.20-41             purrr_0.3.4                
 [76] GenomicAlignments_1.26.0    htmlwidgets_1.5.3           bit_4.0.4                  
 [79] tidyselect_1.1.0            magrittr_2.0.1              R6_2.5.0                   
 [82] generics_0.1.0              Hmisc_4.5-0                 DelayedArray_0.16.2        
 [85] DBI_1.1.1                   pillar_1.5.1                foreign_0.8-81             
 [88] survival_3.2-10             RCurl_1.98-1.3              nnet_7.3-15                
 [91] tibble_3.1.0                crayon_1.4.1                utf8_1.2.1                 
 [94] BiocFileCache_1.14.0        rmarkdown_2.7               jpeg_0.1-8.1               
 [97] progress_1.2.2              data.table_1.14.0           blob_1.2.1                 
[100] digest_0.6.27               openssl_1.4.3               munsell_0.5.0              
[103] Gviz_1.34.1                 askpass_1.1
BSgenome • 148 views
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2
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@herve-pages-1542
Last seen 4 minutes ago
Seattle, WA, United States

Hi,

You need to specify the circ_seqs field in your seed file.

forgeBSgenomeDataPkg() needs to know which sequences are circular and which are not. So if you don't specify the circ_seqs field it tries to get this information by calling GenomeInfoDb::Seqinfo(genome="astMex2NC"). However this only works for NCBI assemblies and UCSC genomes that are _registered_ in GenomeInfoDb.

See here for a similar discussion.

I've tried to clarify this in the BSgenomeForge.Rnw vignette in BSgenome 1.59.3 (devel).

Best,

H.

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Thanks very much. This was a test genome with a single chromosome, so setting circ_seqs: "" solved it. So I guess this means circ_seqs is no longer an optional field (for custom genomes).

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Don't use circ_seqs: "". If it worked it was just luck. See the updated vignette for what to use when there are no circular sequences.

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I looked at your link for the updated vignette, but I wasn't sure I understood it (unrendered). If there are no circular sequences, we should set is like so: circ_seqs: character(0) ?

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From the updated vignette (unrendered):

If the assembly or genome has no circular sequence, set \code{circ_seqs} to \code{character(0)}.

So yes: circ_seqs: character(0).

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