[mira_talk] Re: Mapping assembly

  • From: Lionel Guy <guy.lionel@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 14 Oct 2009 10:45:53 +0200

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


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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