Hello, I am trying to forge a genome for a non-model organism.

I have generated the following seed file (in dcf format) and using the available Athaliana seed file as an example.

Package: BSgenome.Bnapus.NCBI.Bra_napus_v2.0

Title: Full genome sequences for Brassica napus (Bra_napus_v2.0)

Description: Full genome sequences for Brassica napus as provided by NCBI (Bra_napus_v2.0, RefSeq assembly accession: GCF_000686985.2)

Version: 1.0.0

organism: Brassica napus

common_name: Rape

genome: Bra_napus_v2.0

provider: NCBI

release_date: 2017/09/22

source_url: https://www.ncbi.nlm.nih.gov/assembly/GCF_000686985.2

organism_biocview: Brassica_napus

seqnames: c("GCF_000686985.2_Bra_napus_v2.0_genomic.fa")

BSgenomeObjname: Bnapus

SrcDataFiles: GCF_000686985.2_Bra_napus_v2.0_genomic.fna.gz from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Brassica_napus/latest_assembly_versions/GCF_000686985.2_Bra_napus_v2.0/GCF_000686985.2_Bra_napus_v2.0_genomic.fna.gz

PkgExamples: genome[["1"]]

seqs_srcdir: /home/edytas/scratch/bnapus_genome/BSgenomeForge/seqs_srcdir

ondisk_seq_format: fa

I have created a seqs_srcdir directory which contains my seed file as well as the genome fasta file GCF_000686985.2_Bra_napus_v2.0_genomic.fa. When I try to forge the genome I receive the error below. Any help or insights would be very much appreciated.

forgeBSgenomeDataPkg("bnapus_seed.dcf")
Error in .make_Seqinfo_from_genome(genome) : 
  "Bra_napus_v2.0" 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)

sessionInfo( )

``` R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

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

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] BiocParallel_1.24.1 GenomicAlignments_1.26.0
[3] SummarizedExperiment_1.20.0 MatrixGenerics_1.2.0
[5] matrixStats_0.57.0 GenomicFeatures_1.42.1
[7] AnnotationDbi_1.52.0 Biobase_2.50.0
[9] Rsamtools_2.6.0 BiocManager_1.30.10
[11] BSgenome_1.58.0 rtracklayer_1.50.0
[13] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
[15] stringr_1.4.0 Biostrings_2.58.0
[17] XVector_0.30.0 IRanges_2.24.1
[19] S4Vectors_0.28.1 BiocGenerics_0.36.0

loaded via a namespace (and not attached): [1] progress_1.2.2 tidyselect_1.1.0 purrr_0.3.4
[4] lattice_0.20-41 vctrs_0.3.5 generics_0.1.0
[7] BiocFileCache_1.14.0 blob_1.2.1 XML_3.99-0.5
[10] rlang_0.4.9 pillar_1.4.7 glue_1.4.2
[13] DBI_1.1.0 rappdirs_0.3.1 bit64_4.0.5
[16] dbplyr_2.0.0 GenomeInfoDbData_1.2.4 lifecycle_0.2.0
[19] zlibbioc_1.36.0 memoise_1.1.0 biomaRt_2.46.0
[22] curl_4.3 Rcpp_1.0.5 openssl_1.4.3
[25] DelayedArray_0.16.0 bit_4.0.4 hms_0.5.3
[28] askpass_1.1 digest_0.6.27 stringi_1.5.3
[31] dplyr_1.0.2 grid_4.0.2 tools_4.0.2
[34] bitops_1.0-6 magrittr_2.0.1 RCurl_1.98-1.2
[37] RSQLite_2.2.1 tibble_3.0.4 crayon_1.3.4
[40] pkgconfig_2.0.3 ellipsis_0.3.1 Matrix_1.2-18
[43] xml2_1.3.2 prettyunits_1.1.1 assertthat_0.2.1
[46] httr_1.4.2 R6_2.5.0 compiler_4.0.2

Hi,

Ideally you'd want to convert the big FASTA file provided by NCBI to the 2bit format, and use that to forge your BSgenome data package. There are some examples of how to do this in the inst/extdata/GentlemanLab/BSgenome.Amellifera.NCBI.AmelHAv3.1-tools/ and inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/ folders in the BSgenome package (see the fasta_to_sorted_2bit.R script in those folders).

I've registered Bra_napus_v2.0 in GenomeInfoDb 1.26.7 (release) and GenomeInfoDb 1.27.11 (devel) so this should help. This assembly has 1471 sequences so specifying the seqnames in the seed file would be tricky. Both versions should become available via BiocManager::install() in about 36h.

You'll need to specify seqfile_name in your seed file. Take a look at the seed files that were used to forge BSgenome.Amellifera.NCBI.AmelHAv3.1 and BSgenome.Gmellonella.NCBI.ASM364042v2. They are in the inst/extdata/GentlemanLab/ folder. Your seed file should look very similar.

Cheers,

H.

Try adding the seqnames argument to your seed file. The vignette says it's optional, but there is this part to forgeBSgenomeDataPkg:

 seqnames <- x@seqnames
    if (!is.na(seqnames)) {
        .seqnames <- eval(parse(text = seqnames))
    }
    else {
        if (is.na(x@seqfile_name)) {
            .seqnames <- seqlevels(Seqinfo(genome = x@genome))
        }
        else {
            .seqnames <- NULL

And you aren't passing in a seqnames argument, nor a seqfile_name argument, so it's gonna call Seqinfo on your genome, which does this:

> Seqinfo(genome = "Bra_napus_v2.0")
Error in .make_Seqinfo_from_genome(genome) : 
  "Bra_napus_v2.0" 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)

Which you already saw...