Flye assembly of a bacterial genome stuck

Question

[A_heath]

Hi all,

I am using Flye to perform a genome assembly of a bacterial genome. I have raw datas obtained from Ox Nanopore sequencing in fastq format. I ran this command line:

flye --nano-raw /home/.../raw_reads/*.fastq --out-dir /home/.../output

Everything seemed to work fine until after the step: Median overlap divergence

This is what I currently have :

[2021-06-01 10:49:46] INFO: Starting Flye 2.8.3-b1695
[2021-06-01 10:49:46] INFO: >>>STAGE: configure 
[2021-06-01 10:49:46] INFO: Configuring run 
[2021-06-01 10:49:50] INFO: Total read length: 954207277 
[2021-06-01 10:49:50] INFO: Reads N50/N90: 12760 / 3279 
[2021-06-01 10:49:50] INFO: Minimum overlap set to 3000 
[2021-06-01 10:49:50] INFO: >>>STAGE: assembly [2021-06-01 10:49:50] INFO: Assembling disjointigs
[2021-06-01 10:49:50] INFO: Reading sequences 
[2021-06-01 10:49:55] INFO: Counting k-mers: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2021-06-01 10:53:43] INFO: Filling index table (1/2) 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%  
[2021-06-01 11:00:00] INFO: Filling index table (2/2) 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2021-06-01 11:11:46] INFO: Extending reads
[2021-06-01 11:16:58] INFO: Overlap-based coverage: 970 
[2021-06-01 11:16:58] INFO: Median overlap divergence: 0.120684 0%

It stays stuck at this step for several hours now.

Is there a way to solve this issue?

Thank you so much for your help!

Audrey

[GenoMax]

As long as you can see that the program is using CPU cycles (open a new terminal and look at top) you just need to be patient. Assemblies are not a trivial task and can take many hours to complete depending on size of data and hardware resources you are using.

[A_heath]

Thank you for your reply Genomax.

[2021-06-01 15:20:34] INFO: Assembled 0 disjointigs
[2021-06-01 15:20:34] INFO: Generating sequence
[2021-06-01 15:20:34] ERROR: No disjointigs were assembled - please check if the read type and genome size parameters are correct
[2021-06-01 15:20:34] ERROR: Pipeline aborted

Indeed, I just had to wait few more minutes... However, the pipeline aborted and I have no idea why. Can you help me?

[GenoMax]

Someone more familiar with flye will be along but browsing past threads may offer some insight.

[andres.firrincieli]

Hello Audrey

perhaps this could help: link