[mira_talk] Solexa paired ends and 454 single reads

Hello,
I want to use Mira for assembly of 454 reads combined with solexa paired end reads. However, the assembling was started two days ago with:

mira -project=pp -job=denovo,genome,accurate,454,solexa -GE:amm=no SOLEXA_SETTINGS -GE:tismin=2500:tismax=3500

and still hasn't finished. I have noticed that a huge number of paired ends were discarded because they were too short :

AAA/2 too small even with paired end

Is this because their ends might have been clipped. In the project_int_clippings.0.txt there are messages like :

proposed cutback 1b:  left AAA/2        9 -> 24

If I use the noclipping command, would it make the run more accurate? Is it normal that the run takes more than two days (if i need half a day to assemble the 454 reads without the paired ends)?
Thanks a lot,
Mihaela



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