help with setting up local BLAST - (Aug/15/2006 )
hello kind people,
I'm trying to do a local BLAST of the newly created pea aphid genome, using the standalone blast downloads from NCBI and trace archive of the aphid genome. It seems like everything has been set up, but when I run it, the output file just says searching and the command line prompt is returned. I'll try to give a good history to help in the diagnosis.
I've downloaded the BLAST suite, formatted and concatenated the 3 aphid genome files into 1 file, wrote the path file (blast.ncbirc), etc. After formatting, the genome file has been rendered into 5 files with the following extensions: aphidgenome.fasta.nhr, .nin, .nsd, .nsi, and .nsq
Great. Running from Terminal on OS X.4, I try the "blastall" executable with the proper arguments [-p tblastn -d (the location of aphidgenome.fasta on my computer) -i (location of my protein fasta file query on my computer) -o my_output_file.QUERY]
Like I mentioned, a normal-looking output file is started, but it ends with "Searching...". No results afterward, and the command line prompt in Terminal returns. Seems like something has aborted, but I can't determine what or where.
Any ideas or experience with this? Any other info you would like to know? I would greatly appreciate any advice/troubleshooting!
best,
dayalan
I'm trying to do a local BLAST of the newly created pea aphid genome, using the standalone blast downloads from NCBI and trace archive of the aphid genome. It seems like everything has been set up, but when I run it, the output file just says searching and the command line prompt is returned. I'll try to give a good history to help in the diagnosis.
I've downloaded the BLAST suite, formatted and concatenated the 3 aphid genome files into 1 file, wrote the path file (blast.ncbirc), etc. After formatting, the genome file has been rendered into 5 files with the following extensions: aphidgenome.fasta.nhr, .nin, .nsd, .nsi, and .nsq
Great. Running from Terminal on OS X.4, I try the "blastall" executable with the proper arguments [-p tblastn -d (the location of aphidgenome.fasta on my computer) -i (location of my protein fasta file query on my computer) -o my_output_file.QUERY]
Like I mentioned, a normal-looking output file is started, but it ends with "Searching...". No results afterward, and the command line prompt in Terminal returns. Seems like something has aborted, but I can't determine what or where.
Any ideas or experience with this? Any other info you would like to know? I would greatly appreciate any advice/troubleshooting!
best,
dayalan
Hi there,
I had a similar problem when trying to run blast on OS X (Tiger) and Windows XP..... I think blast is a little temperamental when it comes to running on these platforms. I'd say a better option is to run it on a Unix platform.....it works very well.
Good luck!
I generally haven't had any problems running blast. All you need is the ncbi-toolbox, this contains multiple programs like blastclust blastpgp and formatdb.
Download this to your machine, use formatdb to setup your databases (it looks like you have already done this correclty). Now simply use the default setup of the blastpgp program.
scruffy@joshua > ./blastpgp -d ../masked-db -i seq/1A12A.seq -Q 1A12A.mat
should run my quesry sequence against the masked-db. The -Q switch will produce a PSSM, which you should keep and a -O should give you the fragment alignments.
Sorry you're having difficulties, dgs74 -- I've hesitated replying to this thread because (like perlmunky) I've had very little difficulty using BLAST, but I've only done so on Windows and Linux machines -- I don't know about the Mac version.
I'd suspect that it's be very similar to the Linux version, as the Mac OS is really just BDS Unix with an Apple-designed GUI...