[mira_talk] Re: Memory problem with MIRA

On Donnerstag 03 Dezember 2009 ankit gupta wrote:
> I am trying to use mira for a de novo assembly of a transcriptome but after
> running for a few minutes, it gives me a memory related error.
> 
>      Writing temporary hstat files:
>      [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%] done
> 
>      Analysing hstat files:
>      [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
>      Ouch, out of memory detected.
> 
> My data is from 454 GS FLX Titanium series and I have nearly 650,000 reads
> with associated quality file. I am using a strong server with 32 gb RAM.
>  Any idea why this might be happening?

Hello Ankit,

ummmm ... it throws an out of memory during the analysis of the hashes? This 
is ... peculiar. Am I right in guessing that these are not genomic reads but 
EST?

Can you please give me an "ls -l" of the log directory, I'd like to check the 
size of the files.

> I am using the following command to run mira:
>      mira -project=1TCA --job=denovo,est,normal,454 -fasta -notraceinfo
> -noclipping >&log_assembly.txt

Oh, yeah, right, ESTs. There it is.

Well, you are using "--noclipping" to kill off all the clips. Why? At least 
the Poly-A/Poly-T clip should be on in EST assemblies, else this will lead you 
nowehere (or into memory problems :-)

> Also I am unable to figure out how to invoke the miraMEM memory call. When
>  I try giving this as command, my shell returns with command not found and
>  mira doesn't seem to accept is as an option or argument. Can you tell me
>  what linux command should I give to invoke miraMEM to get an estimate of
>  how much memory my project might need ?

'miramem'. If you downloaded the binary distribution, you'll see it in the 
'bin' directory, realised as link to 'mira'. If you compiled yourself: create 
a symbolic link from mira to miramem (ln -s mira miramem).

Regards,
  Bastien

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