[mira_talk] Re: Mapping assembly

Mmh... I still think the number of skims is fishy, but can't give further hypothesis if you say that the repeats are masked and reads are trimmed. I'm afraid you'll have to wait for Bastien's answer...


Just by curiosity, what pass is mira in? Has it gone through the first one at least?

L.


On 14 Oct 2009, at 12:47 , Brian Forde wrote:

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 ...
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============================================
Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala

phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
============================================


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