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SPAdes taking hours (Read 2359 times)
Jun 12th, 2020 at 8:06am

Bte   Offline
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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
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Reply #1 - Jun 13th, 2020 at 11:03pm

Dmitrii Sukhomlinov   Offline
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Posts: 77
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?

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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