Biostar Test Site

This is site is used for testing only. Visit: https://www.biostars.org to ask a question.

Flye assembly of a bacterial genome stuck
0
0
Entering edit mode
12 days ago
Audrey ▴ 60

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

assembly Flye • 46 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 199 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6