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Mira4 Assembler Taking Too Long Time And Using All Memory For Denovo, Est Assembly

Hi Fellows,

My PC has 48 GB of RAM and 8 CPU. I am trying to create denovo assembly using Mira 4 Assembler. Input file has only 2 fastq files with only 30 million reads with sequence length 50-350 nt.

I used below manifest.comf file

project = miraproject
job = est, denovo, accurate
parameters = COMMON_SETTINGS -GENERAL:number_of_threads=4 amm=off -HS:mnr=yes:nrr=8

parameters = IONTOR_SETTINGS -CL:qc=no -ALIGN: min_relative_score=90 -ASSEMBLY:minimum_read_length=200

readgroup = SomeUnpairedIonTorrentReadsIGotFromTheLab

technology = iontor

data = /media/DATAPART3/Combine_Files/miraproject/data/

But problem is it is taking long time more than 20 hours and it is using all the memory.

Any suggestion?

I would really appreciate your help.

Thanks in advance.

Naresh

est ion-torrent rna-seq
• 4,796 views • link
updated by Ram Ram • written by nbvasani nbvasani

What do you think Mira4 is doing? I suggest running with a subset of your fastq, only measure the time it takes to run {2 or 4 or 8} thousands of reads instead of 30,000,000. Plot those times on a graph and make the estimate.

• 0 views • link
written by karl.stamm karl.stamm

This is first time I am running mira4 assembler. So I am not sure what it is doing. It is using all PC memory. But this 2 fastq file are subset of my input file.

• 0 views • link
written by nbvasani nbvasani

1 answer

You could try to run the miramem tool that is distributed with mira to compute the memory requirements and see if the amount of memory used is expected.

If you want to tune your paramters to use less memory and/or time I suggst you post on the MIRA mailng list.

• 0 views • link
written by lelle lelle

Thanks Lelle.....

• 0 views • link
written by nbvasani nbvasani

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