getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there....
Entering edit mode
Last seen 3.5 years ago


I am trying to forge a genome into BSgenome... but I am failing so far...every time I get different errors, but I am very stucked now with the following error message:

Error in getSeqSrcpaths(seqname, prefix = prefix, suffix = suffix, seqssrcdir = seqssrcdir) : file(s) not found: /data/fg2/guerrero/cheetahmethylation/MeDIPStest/genome/scaffolds/AciJub2NW_015130604.1.fasta

Which I have no idea how to solve, since my files (collection of fasta files, one per sequence to fogre) is in that very same folder and the file listed in the error as "not found", is exactly the first one in the folder... I thought it was a typo matter...but it seems not... I dunno if it has to do with the format I am using to define the seqnames in the seed file which looks like this:

*It seems that when posting it the underscores between characters are gone... which make it seem as though it's a typo error... but I swear is not...

seqnames: paste("NW0",seq(from=15130604,to=15144985,by=1),".1", sep="") seqfilesprefix: AciJub2 seqfiles_suffix: .fasta

I hope someone can give me any hints on this... it is also the first time I work with Bioconductor...

Cheers and thanks, :)

bsgenome forgebsgenome getSeqSrcpaths • 437 views
Entering edit mode

Please edit your post to make proper use of markdown so underscores and other important characters don't disappear. For example wrap file paths and R expressions in backquotes (`) so we can see exactly what they look like and even copy/paste them in our own R sessions. This should give something like this /data/fg2/guerrero/cheetah_methylation/MeDIPS_test/genome/scaffolds/AciJub2NW_015130604.1.fasta, or like this seqnames: paste("NW_0",seq(from=15130604,to=15144985,by=1),".1", sep=""), or like this seqfiles_prefix: AciJub2.

Even better, I would suggest that you show us the full content of your seed file by copy-pasting it here, and then to place a line with 3 backquotes on their own (```) above and below the content of the seed file. Thanks!


Login before adding your answer.

Traffic: 358 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6