Question

Error in Forge the target package (BSgenome)

0

Entering edit mode

jiazhou0116 • 0

@jiazhou0116-24087

Last seen 17 months ago

Netherlands

Hi,

I am trying to forge a BSgenome according to the instruction https://www.bioconductor.org/packages/devel/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf. But I have error in checking the package with:

R CMD check <tarball>

where <tarball> is the path to the tarball produced by R CMD build.

* installing *source* package ‘BSgenome.Rhinella.marina.UNSW.RM170330’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning in .seqlengths_TwoBitFile(x) :
  /Users/jiazhou/Box/methylation_analysis/msgbsR/BSgenome.Rhinella.marina/BSgenome.Rhinella.marina.UNSW.RM170330.Rcheck/00LOCK-BSgenome.Rhinella.marina.UNSW.RM170330/00new/BSgenome.Rhinella.marina.UNSW.RM170330/extdata/single_sequences.2bit doesn't have a valid twoBitSig
Error: package or namespace load failed for ‘BSgenome.Rhinella.marina.UNSW.RM170330’:
 .onLoad failed in loadNamespace() for 'BSgenome.Rhinella.marina.UNSW.RM170330', details:
  call: h(simpleError(msg, call))
  error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': UCSC library operation failed
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/jiazhou/Box/methylation_analysis/msgbsR/BSgenome.Rhinella.marina/BSgenome.Rhinella.marina.UNSW.RM170330.Rcheck/BSgenome.Rhinella.marina.UNSW.RM170330’

Just wondering whether anyone have suggestions for it.

Thanks,

Jia

software error BSgenome • 1.7k views

ADD COMMENT • link 4.2 years ago • updated 4.0 years ago jiazhou0116 • 0

0

Entering edit mode

This error has been fixed by slicing the reference genome file into multiple .fas files per scaffold/chromossome.

ADD REPLY • link 4.0 years ago jiazhou0116 • 0

score 0 · Answer 1 · 2020-09-03

0

Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 7 hours ago

United States

Looks like you have a corrupted 2bit file. Maybe try downloading it again?

ADD COMMENT • link 4.2 years ago James W. MacDonald 67k

0

Entering edit mode

Hi James,

Thanks for your reply. The 2bit file was generated during the step

> forgeBSgenomeDataPkg("path/to/my/seed")

The issue could be I did not slice my reference genome file into multiple .fas files per scaffold/chromossome as mentioned in the instruction. Will try whether this solves the error.

The sequence data must be in a single twoBit file (e.g. musFur1.2bit) or in a collection of FASTA files (possibly gzip-compressed). If the latter, then you need 1 FASTA file per sequence that you want to put in the target package. In that case the name of each FASTA file must be of the form <prefix><seqname><suffix> where <seqname> is the name of the sequence in it and <prefix> and <suffix> are a prefix and a suffix (possibly empty) that are the same for all the FASTA files.

Thanks,

Jia

ADD REPLY • link 4.2 years ago jiazhou0116 • 0