On Fri, Mar 21, 2014 at 5:42 AM, Nilaksha Neththikumara
<nilakshafree...@gmail.com> wrote:
> Thank you very much. I was able to download blast locally and configure the
> loc. file so now it is up and running. :) But another problem encountered
> when I'm trying to align a fasta file with 4mb, giving an error called
> blastn(708,0xa03ca1a8) malloc: *** mach_vm_map(size=1048576) failed (error
> code=3)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Bus error: 10
> I referred a bit and the only solution i could come across was that it is
> some kind of an error encountered when overloading the memory of a single
> thread.

It does sounds like a memory (RAM) problem, yes. However in general
using more threads will not save memory (it may even need more).

> So I quit galaxy, jumped into the terminal and performed the same
> task with num_threads =16 (my mac pro got two quad cores with virtual dual
> cores : 2*4*2 =16) So far good.

Stange. Perhaps you had some other memory hungry tasks running
before at the same time as the failed BLAST?

> When examining the code in galaxy it was using a value called
> ${GALAXY_SLOTS:-4} to the num_thread argument yet I'm
> sure it only utilised a single core. Can I configure it to use all the 16
> cores? Any advice please?

Bjoern answered that; This would have defaulted to 4 threads if
the GALAXY_SLOTS setting wasn't setup.

> PS: Since my new questions are out of track with my first question (blast+
> wrapper with remote searching) do I need to start a new thread? Sorry if I'm
> doing anything wrong here. I'm just very new and novice. (got my appointment
> in the beginning of March right after my graduation , no body is familiar
> with bioinformatics here in Sri Lanka, so I'm struggling to make my move
> alone with the help of you all over the world )

Yes, next time you have a completely new question, start a new thread.

Also try reading the forums at seqanswers.com and Q&A at biostars.org


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