Hi!

I am trying to forge a BSgenome package for the most current Dmel6 genome using the FASTA file from Ensembl (BDGP6.32 v104). However, the package will not install and stops with an error:

* installing *source* package ‘BSgenome.Dmelanogaster.6.32’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: package ‘BiocGenerics’ was built under R version 4.0.5 
2: package ‘GenomeInfoDb’ was built under R version 4.0.5 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: package ‘BiocGenerics’ was built under R version 4.0.5
Warning: package ‘GenomeInfoDb’ was built under R version 4.0.5
Error: package or namespace load failed for ‘BSgenome.Dmelanogaster.6.32’:
 .onLoad failed in loadNamespace() for 'BSgenome.Dmelanogaster.6.32', details:
  call: .make_BSgenome_seqinfo(single_sequences, circ_seqs, genome, seqnames)
  error: sequence names found in file '/Users/Geo/BSgenome.Dmelanogaster.6.32.Rcheck/00LOCK-BSgenome.Dmelanogaster.6.32/00new/BSgenome.Dmelanogaster.6.32/extdata/single_sequences.2bit' are not identical to 'seqnames'. May be the data on disk is corrupted?
Error: loading failed
Execution halted
ERROR: loading failed

I prepared the genome FASTA and created the 2bit file as follows:

library(Biostrings)

dna <- readDNAStringSet("Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa.gz")

### Check seqnames.
current_SequenceName <- unlist(heads(strsplit(names(dna), " ", fixed=TRUE), n=1L))

names(dna) <- current_SequenceName

### Export as 2bit.
library(rtracklayer)
export.2bit(dna, "Dmel632.2bit")

Using the original sequence names or shortened names appeared not to make a difference. Any advice would be greatly appreciated!

Geo

Hi,

Any reason you can't use the BSgenome.Dmelanogaster.UCSC.dm6 package?

What Ensembl calls the "BDGP6.32" assembly has GenBank accession GCA_000001215.4 and RefSeq accession GCF_000001215.4. This is what NCBI calls the "Release 6 plus ISO1 MT" assembly and what UCSC calls the "dm6" genome. The only difference between BDGP6.32 and dm6 are the sequence names. BDGP6.32 and Release 6 plus ISO1 MT use the same sequence names a.k.a. the NCBI sequence names.

Switching from UCSC naming style to NCBI naming style is easy:

library(BSgenome.Dmelanogaster.UCSC.dm6)
seqinfo(BSgenome.Dmelanogaster.UCSC.dm6)
# Seqinfo object with 1870 sequences (1 circular) from dm6 genome:
#  seqnames         seqlengths isCircular genome
#  chr2L              23513712      FALSE    dm6
#  chr2R              25286936      FALSE    dm6
#  chr3L              28110227      FALSE    dm6
#  chr3R              32079331      FALSE    dm6
#  chr4                1348131      FALSE    dm6
#  ...                     ...        ...    ...
#  chrUn_DS485998v1       1003      FALSE    dm6
#  chrUn_DS486002v1       1001      FALSE    dm6
#  chrUn_DS486004v1       1001      FALSE    dm6
#  chrUn_DS486005v1       1001      FALSE    dm6
#  chrUn_DS486008v1       1001      FALSE    dm6

seqlevelsStyle(BSgenome.Dmelanogaster.UCSC.dm6) <- "NCBI"
seqinfo(BSgenome.Dmelanogaster.UCSC.dm6)
# Seqinfo object with 1870 sequences (1 circular) from Release 6 plus ISO1 MT genome:
#   seqnames        seqlengths isCircular                 genome
#   2L                23513712      FALSE Release 6 plus ISO1 MT
#   2R                25286936      FALSE Release 6 plus ISO1 MT
#   3L                28110227      FALSE Release 6 plus ISO1 MT
#   3R                32079331      FALSE Release 6 plus ISO1 MT
#   4                  1348131      FALSE Release 6 plus ISO1 MT
#   ...                    ...        ...                    ...
#   211000022278074       1003      FALSE Release 6 plus ISO1 MT
#   211000022278179       1001      FALSE Release 6 plus ISO1 MT
#   211000022279016       1001      FALSE Release 6 plus ISO1 MT
#   211000022278576       1001      FALSE Release 6 plus ISO1 MT
#   211000022278384       1001      FALSE Release 6 plus ISO1 MT

FWIW here is how you can check that BDGP6.32 uses the NCBI sequence names:

library(GenomeInfoDb)
chrominfo <- getChromInfoFromEnsembl("BDGP6.32", map.NCBI=TRUE)
identical(chrominfo$name, chrominfo$NCBI.SequenceName)  # TRUE

Hope this helps,

H.