error when forging a BSgenome
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Entering edit mode
Didi ▴ 10
@didi-10905
Last seen 9 months ago

Hi,

When forging a BSgenome I'm getting this error :

> "Error in .readSeedFile(x, verbose = verbose) :    seed file
> 'SARSCOV2-seed' must have exactly 1 record"

This is the code I'm running:

> library(BSgenome)  myfile <- read.dcf("seed_file.txt", fields = NULL,
> all = FALSE, keep.white = NULL) write.dcf(myfile , file = "seed.dcf",
> append = FALSE, useBytes = FALSE, indent = 0.1 * getOption("width"),
> width = 0.9 * getOption("width"),keep.white = NULL) 
> forgeBSgenomeDataPkg("seed.dcf")

Please can you tell me what I'm doing wrong?

Thanks a lot.

BSgenome • 194 views
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Entering edit mode

Hard to tell without seeing your seed file.

Not sure what you are trying to do with your read.dcf() and write.dcf() calls. It just seems like an unnecessary complication that can only backfire to me. Please try to follow the instructions in the How to forge a BSgenome data package vignette as close as possible. The vignette shows how to create the seed file directly as a DCF file. Note that a DCF file is a text file so it doesn't make sense to first create the file with a .txt extension to then try to convert it to DCF with read.dcf() and write.dcf().

Also showing your sessionInfo() like instructed in our Posting Guide wouldn't hurt.

Thanks,

H.

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