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Old 01-29-2020, 05:55 AM   #1
Junior Member
Location: UK

Join Date: Aug 2013
Posts: 6
Default SOAPdenovo2 long run

Hello all,
Iím trying to assemble a plant genome (this is my first time). I have 100bp PE reads (106G forward and 106G reverse). Iím using soapdenovo2 to assemble the data on a cluster. The job was running on 10 nodes with each using 20 threads and 80Gb of memory. The maximum amount of time allowed for a job is 7 days.
I tried the following script however the job does not finish in the allotted time
SOAPdenovo-63mer all -s ./soap.config -K 63 -R -o genome

So then I tried to build it in parts using the script below, but even this does not finish
SOAPdenovo-63mer pregraph -s ./soap.config -K 63 -R -o genome

If using more computer resources or getting my time limit extended is not an option, how can I assemble the genome?

I tried using DMTCP to checkpoint the run so that I can resubmit the run and continue the assembly after the 7 days but I cannot get DMTCP to work with soapdenovo2.

I would be grateful for any assistance
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Old 01-30-2020, 04:26 PM   #2
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Location: Eugene, OR

Join Date: May 2013
Posts: 521

I'd try a speedy assembler like BBtools as a first pass just to see what a rough draft looks like. A slower assembler but one that should finish in a day is abyss-pe with the bloom filter option enabled.
Providing nextRAD genotyping and PacBio sequencing services.
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Old 01-31-2020, 11:01 PM   #3
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Location: UK

Join Date: Aug 2013
Posts: 6

Thanks for the suggestions. I'll give these tools a try
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assembly, checkpoint, dmtcp, long run, soapdenovo2

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