CLC running time for an assembly of 454 reads

mcri13 · 08-23-2013, 11:54 AM

Hi all:

What is the estimated running time of assembling aprox. 71 million of 454
reads using CLC Assembler? We use an iBM HX5 server running Ubuntu with 40 cores and 320GB of RAM.

We have been running the process for over a week and it seems that it has stalled. We did check the status of processor and memory usage and it shows a 99-100% (%CPU) but 0% (%MEM). Wondering why!

Best,

Marco Cristancho
CENICAFE

nickloman · 09-22-2013, 04:18 AM

Hard to predict exactly, but it sounds like something has gone wrong to me. Have you tried Roche's 454 gsAssembler (Newbler) ?

mcri13 · 09-23-2013, 07:59 AM

Hi:

Thanks for your answer. It has been hard to install gsAssembler on our machine. We have a 64-bit running Ubuntu. However, we are still trying the installation, it seems it is our best bet.

Greetings,

Marco

sklages · 09-23-2013, 11:39 AM

What did the CLC support say? It is probably worth asking them.
gsAssembler will install on 64bit Ubuntu, don't worry ..

NextGenSeq · 09-24-2013, 06:30 AM

I de novo assembled a billion Illumina reads and it took a month.

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08-23-2013, 11:54 AM	#1
mcri13 Junior Member Location: Colombia Join Date: Jul 2011 Posts: 2	CLC running time for an assembly of 454 reads Hi all: What is the estimated running time of assembling aprox. 71 million of 454 reads using CLC Assembler? We use an iBM HX5 server running Ubuntu with 40 cores and 320GB of RAM. We have been running the process for over a week and it seems that it has stalled. We did check the status of processor and memory usage and it shows a 99-100% (%CPU) but 0% (%MEM). Wondering why! Best, Marco Cristancho CENICAFE

09-22-2013, 04:18 AM	#2
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	Hard to predict exactly, but it sounds like something has gone wrong to me. Have you tried Roche's 454 gsAssembler (Newbler) ?

09-23-2013, 07:59 AM	#3
mcri13 Junior Member Location: Colombia Join Date: Jul 2011 Posts: 2	Hi: Thanks for your answer. It has been hard to install gsAssembler on our machine. We have a 64-bit running Ubuntu. However, we are still trying the installation, it seems it is our best bet. Greetings, Marco

09-23-2013, 11:39 AM	#4
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	What did the CLC support say? It is probably worth asking them. gsAssembler will install on 64bit Ubuntu, don't worry ..

09-24-2013, 06:30 AM	#5
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 482	I de novo assembled a billion Illumina reads and it took a month.