General Category >> Help and How-to >> SPAdes taking hours

Message started by Bte on Jun 12th, 2020 at 8:06am

Title: SPAdes taking hours
Post by Bte on Jun 12th, 2020 at 8:06am
Hello, this is my first time posting here so please let me know if there is etiquette that i am not aware of. I am trying to assemble 4 sets of paired end sequences in ugene using the Linux version through Ubuntu on my windows laptop. I am using a workflow that reads, trims, and then assembles each pair. Everything is fine until the final step. The workflow has been running for over 5 hours and it has not budged from 92% complete. Is this normal? Should i start over? Any advice is much appreciated

Title: Re: SPAdes taking hours
Post by Dmitrii Sukhomlinov on Jun 13th, 2020 at 11:03pm
Hello. You're OK about the etiquette, don't worry!
As I've understood, you're trying to run the "De novo assembly Illumina PE reads" workflow. The last "Assembly reads with SPAdes" step could require a lot of time, but 5 hours is a bit too much. First of all, left the execution for all night - it's possible, that data you need to process is really very time-consuming. It also depends on the processing power of your computer, so is your machine isn't very quick it definitely could be a bit long. If it won't finish at all, could you, please, share your data with me and I will try to figure it out?

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