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Old 02-10-2015, 02:07 AM   #1
Location: Paris

Join Date: Feb 2014
Posts: 36
Default MIRA denovo assembly


I have a problem with MIRA 4 assembly denovo using reads in fastq format come from ion Torrent technology.

my manifest file is:

project = pDG2
job = denovo
readgroup = lab
data = fastapDG.fastq
technology = iontor

the code used is:

mira manifest.conf>log_assemb5.txt
MIRA works for 10 minutes and afterward the process aborted. This is the last sentence:

HTML Code:
Filtering forward skims.
Localtime: Tue Feb 10 10:46:50 2015
Writing reduced skim file:
 [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] .
Failure, wrapped MIRA process aborted.
I would like having some suggestion to understand where could be my error..
The MIRA result folder is empty and the MIRA info folder contains only 3 warning txt files, of 0 byte each one, called:
pDG2_info_WARNINGS_critical (empty)
pDG2_info_WARNINGS_medium (empty)
pDG2_info_WARNINGS_minor (empty)
pDG2_info_readrepeats.lst (this file contains the read list 119Mb)

I don't know if these informations are enough.
Can I ask also if other programs could sostituite MIRA for this kind of assembling?
Giffredo is offline   Reply With Quote