hardware requirements to run blastX

[litali]

Hi all,
Can anybody give me an estimation what are the hardware requirements to have BlastX locally installed run in a reasonable pace and work ok with 454 data?
Many thanks!!!

[westerman]

"Reasonable" is a hard term to shoot for. How many reads do you want to process in how many hours? I will say that the minimum hardware I would want is an 8-core machine with 4 GB of memory. I suspect that would get through a 454 run -- contigs and singletons -- inside of a week.

[litali]

blast problems

Thank you, another questionL I try to run blast and receive immediately a message: segmentation fault.
What does it mean?

[drio]

It means your program is trying to access a piece of memory that does not belong to it. The hardware complains and tells the OS and the OS sends a signal to the process and dies.

Take a look to see if any core file has been created. That file will have debugging data (stack trace) that can help you to figure out what part of the code caused the problem.

[westerman]

It means your program is trying to access a piece of memory that does not belong to it. The hardware complains and tells the OS and the OS sends a signal to the process and dies.

Take a look to see if any core file has been created. That file will have debugging data (stack trace) that can help you to figure out what part of the code caused the problem.

I doubt if a 'core' file will help a novice user -- especially if they do not have a copy of the blast source code. Heck, I doubt if I even have the chops any more to work with a 'core' file and adb (or debugger of choice.)

I do agree that the seg fault is a memory related problem. Doing a google search on "blast + 'segmentation fault' " brings up over 6000 results. I suspect that one of them will help out 'litali'. My first suggestion is to see if you can run blast using one sequence versus a very small database. In other words reduce your problem down to something simple.

[Torst]

Can anybody give me an estimation what are the hardware requirements to have BlastX locally installed run in a reasonable pace and work ok with 454 data?

What database will you blastx against?
ie. how many sequences/megabases.

What is a reasonable pace?
ie. how many plates of 454 reads do you need to process per week?

[v_kisand]

as kind a intermediate user myself seg fault means to me there is installation/compilation error... usually compilation from source will help.

reasonable pace.... hmmm with my modest Intel(R) Xeon(R) CPU E5420 @ 2.50GHz
and working with 454 too, howeve, bacterial genomes or metagenomes from few plates, when no results with overnight processes I try to find some other solution