Spades has been running for over a week. Normal?

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5.1 years ago

stacy734 ▴ 40

Hi all,

I am running a genome assembly using Spades on a 1GB genome using ~120GB paired-end Illumina reads.

The process has been running for more than a week, mostly on the K-mer counting step. The log shows a notation : "Collecting K-mer information, this takes a while" so maybe this is expected.

Does anyone have similar experiences with Spades run time?

Thanks for any advice, Stacy

spades genome Assembly • 2.3k views

ADD COMMENT • link 5.1 years ago by stacy734 ▴ 40

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Spades can take a long while, I'm surprised it didn't run out of memory. Can you check top to see if the process is indeed running?

ADD REPLY • link 5.1 years ago by Asaf 10k

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Could it be that it is swapping ? Eg install htop and/or glances if on ubuntu and check the hard disk is not being used and RAM is not full.

How much RAM do you have ?

ADD REPLY • link 5.1 years ago by colindaven 7.0k

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I have Spades running on a compute farm with 500G RAM. It is still running and only using 310G of the RAM allowed.

There is plenty of disk space (~4 TB).

I'll just let it roll.

Thanks for your comments!

ADD REPLY • link 5.1 years ago by stacy734 ▴ 40

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In case you have way more coverage than necessary you may want to normalize your data before you do the assembly. Having excessive coverage can be detrimental for assemblies.

ADD REPLY • link 5.1 years ago by GenoMax 148k

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