I wanted to use BEDTools to extract genomic sequences (fastaFromBed).
My BED file has all 24 chromosomes, hence I want to use whole genome (merged from chromosome.fa).
Tried to:
fastaFromBed -fi genome.fa -bed all.chromosomes.bed -fo output
but gotSegmentation fault (core dumped)
Tried to use every chromosome.fa separately and it worked:
fastaFromBed -fi chromosome${i}.fa -bed all.chromosomes.bed -fo output
Of course I am getting annoyingWARNING. chromosome (chr..) was not found in the FASTA file. Skipping.
But it's still better than nothing and really fast.
I prefer to use BEDTools for sequence extraction so I am wondering is it possible to solve this segmentation fault thing?
It seems that large genome.fa file can't be handled by BEDTools as I also tried nucBed and got the same thing or it might be some genome merging problem.EDITED
This is the bed file I used for: intersectBed; closestBed; fastaFromBed ([www.box.com][1]).
There were problems only with fastaFromBed and only when I tried to use the whole genome.fa (~3.15GB). As I mentioned before - used every chromosome separately, got warnings but there was no segmentation fault and output was fine.
I am wandering that it might be genome.fa problem (used cat to me ...