I'm trying to install a local copy of polyphen and one of the stages is to make a blastdb from uniref100.
I ran this command last night and its still going nearly 12 hours later. I don't know if this is normal:
makeblastdb -in uniref100-formatted.fasta -dbtype prot -out uniref -title 'UniRef100 2010_07, 15-Jun-2010' -parse_seqids
Building a new DB, current time: 11/03/2010 23:51:19 New DB name: uniref New DB title: UniRef100 2010_07, 15-Jun-2010 Sequence type: Protein Keep Linkouts: T Keep MBits: T Maximum file size: 1073741824B
The program just seems to be sitting there. The uniref file is 233GB so I don't expect it to be quick but I wasn't expecting 12 hours. I am running linux on a virtual machine on an external hard drive with only 1 gig of RAM so its not on the fastest machine in the world either.