Re: [AMOS-help] help w/AMOScmp & subsequent Hawkeye crashes

[Jonathan E. <Jon...@ni...>]

No, we are only using ~2000 simulated reads.  It must be something else.

Thanks to you both, Adam&Lionel.

Jonathan


Adam Phillippy wrote:
> Hi Jonathan,
> Is it a memory issue as Lionel suggests? Or something else?
>
> Best,
> Adam
>
> On Fri, Jun 20, 2008 at 11:05 AM, Lionel Guy <guy...@gm... 
> <mailto:guy...@gm...>> wrote:
>
>     Hi Jonathan,
>
>     Just curious... how many reads do you have? have you watched your
>     computer memory when loading hawkeye? I crashed hawkeye once, and the
>     probable reason was that there was another application running on the
>     same server, that ate all the memory...
>
>     You may want to check what "top" says at the time you launch hawkeye,
>     for example:
>
>     hawkeye OurPombe.bnk &; top
>
>     Regards,
>
>     Lionel
>
>     Jonathan Epstein wrote:
>     > Hi Adam, Mike et al,
>     >
>     > While we wait for the imminent arrival of some real S. pombe Solexa
>     > data, we are simulating our own reads from S. pombe and trying to
>     > align them to the published S. pombe genome.
>     >
>     > Our workflow was like this:
>     >
>     > * generated our own multi-FASTA file of three chromosomes of S.
>     pombe
>     >  (note that there are a total of ~7 contigs, which are glued
>     together
>     >  within chromosomes with a run of 100 Ns) * created a multi-FASTA
>     > file of simulated reads, fasta.fakereads * Converted fasta.fakereads
>     > (fasta must go first in the name) into afg format using
>     tarchive2amos
>     >  * ran
>     >
>     > AMOScmp -D "TGT=fakereads.afg" -D "REF=fasta.referenceGenome"
>     > OurPOMBE
>     >
>     >
>     > * loaded OurPOMBE.bnk into Hawkeye (which runs fine with some of our
>     > other datasets) and watched it crash
>     >
>     >
>     >
>     > We don't know whether our workflow is wrong, or whether there's
>     a bug
>     > in Hawkeye and/or AMOScmp, or something else
>     >
>     > At this point, all of the data is simulated and/or public, so we
>     > would be glad/grateful to send you the data so perhaps you can see
>     > where we're going wrong.
>     >
>     > We also wonder whether we need to be dealing explicitly with the S.
>     > pombe contigs rather than its chromosomes; perhaps the multiple Ns
>     > described above are giving AMOS indigestion.
>     >
>     >
>     > Thanks,
>     >
>     > Jonathan
>     >
>     >
>     >
>     >
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