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Giffredo 02-10-2015 02:07 AM

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?

westerman 02-10-2015 06:52 AM

Sending email to the MIRA list is useful. You may need to sign up for it.

As for a guess as to the problem I'd say a lack of memory since you never got to the '[100%]' part. What is the size of the machine you are using?

You will probably have to dig through the entire log file to see if there is some upstream error causing problems.

Giffredo 02-11-2015 01:26 AM

Yes, thank you!
it was a problem linked with the lack of memory. Now it works well!

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