[mira_talk] RE :Assembly stopped
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 24 Aug 2011 22:55:09 +0200
Oh, I suspect your process got killed by the kernel due to memory shortage ...
165m reads really is outside the specs of MIRA.
B.Artemus Harper <subanark@xxxxxxxxx> a écrit :I'm not sure what happened. The
assembly simply stopped without errors or finishing its job.
I ran with:
mira --project=Chemdawg_mira_1 --job=genome,solexa SOLEXA_SETTINGS
-FN:fqi=Medicinalgenomics.com_Prep7_1-1_sequences.txt -GE:tismin=150,tismax=400
And here is the last output generated.
Have read pool with 165481300 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 165481300 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 165481300 0
Avg tot rlen 0 0 0 0 101 0
Avg rlen used 0 0 0 0 100 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 165481300 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:16878835765 used bases in used reads: 16713354465
Solid total bases:0 used bases in used reads: 0
===========================================================================
Starting Solexa known adaptor right clip ... Localtime: Wed Aug 24 11:45:49 2011
Searching multithread now ...
2
Searching for Solexa partial end adaptors ...
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done. Clipped 1361712 reads.
Starting minimum quality threshold clip ... done. Killed 450609 reads.
Clipping dubious poly-base stretches at end of reads ... done.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 165481300 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 164691373 0
Avg tot rlen 0 0 0 0 101 0
Avg rlen used 0 0 0 0 100 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 161529201 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:16878835765 used bases in used reads: 16556634303
Solid total bases:0 used bases in used reads: 0
===========================================================================
--
Artemus Harper
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