[mira_talk] Re: Mapping assembly

sorry yes it is still running. I am assuming that the data is highly
repetitive but I have repeat masked it. The data is trimmed and includes a
traceinfo file

On Wed, Oct 14, 2009 at 11:44 AM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:

> Sounds strange indeed... Should have completed by now. I'm not completely
> familiar with the gears of mira, but it seems to me that you have a huge
> amount of skims (hits, if I'm correct) for your number of reads... do you
> have highly repeated data? Non-trimmed data?
>
> And by the way, is the mira process still alive?
>
> Lionel
>
>
> On 14 Oct 2009, at 10:52 , Brian Forde wrote:
>
>  Hi lionel,
>>
>> I have approx only 550,000 reads. Its a 454 project only. I am assuming
>> that it has stalled as memory usage is down to 1%. From what you are saying
>> it appears to me that some thing has gone wrong.
>>
>> Brian
>>
>>
>> On Wed, Oct 14, 2009 at 9:45 AM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:
>> Hi Brian,
>>
>> What pass are you in? (grep "Pass" assembly_log.txt) How many reads do you
>> have (looks like an awful lot)? Is the process terminated (ps -A | grep
>> mira)?
>>
>> My guess is that you have a zillion reads and mira is still sorting reads.
>> It has loaded 2.7 Giga-skims (elements), so that might take some time to
>> sort... in my genome, I have 3 M reads and I get about 34 Mega-skims, i.e.
>> 100 times less...
>>
>> Hope that helps
>>
>> Lionel
>>
>>
>> On 14 Oct 2009, at 10:25 , Brian Forde wrote:
>>
>> I havebeen running a mapping assemblu of a geome for a few days now but it
>> appears to be hanging. I checked it yesteday evening and again this morning
>> and it hasn't moved. I was wondering if it was hanging and if i can quit
>> (losing the assembly in the process).
>>
>> the last entry in the log is
>>
>> De-normalising SKIM hits ... (this will take a while)
>> Loading skims in id range 0 to 213398
>> Loaded 2 773 837 688 elements.
>>
>> Sorting ...
>> --
>> "If scientists knew what they were doing they wouldn't call it research"
>>
>>
>>
>>
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>>
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>> "If scientists knew what they were doing they wouldn't call it research"
>>
>
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