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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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No polished contigs despite ~50X coverage #207

Open gettl008 opened 2 years ago

gettl008 commented 2 years ago

I've used Racon on > 200 assemblies and have only had this error arise with one sample...

The reads in this case are ONT reads that I mapped to my assembly using Minimap2. The coverage distribution (removing the high coverage tail) looks like this... image

When I run Racon, everything looks normal, there are no errors, and it ends with [racon::Polisher::] total = 24.029181 s The output file, however, is empty. When I run with '-u', the output file gets properly filled with all the unpolished contigs.

I'm thinking this has something to do with the input reads as I have two different assemblies I've made for the same sample and both are having the same issue. Any ideas?

rvaser commented 2 years ago

Hello, can you please paste the whole racon log?

Best regards, Robert

gettl008 commented 2 years ago

Of course...

[racon::Polisher::initialize] loaded target sequences 0.072242 s
[racon::Polisher::initialize] loaded sequences 6.214936 s
[racon::Polisher::initialize] loaded overlaps 5.285117 s
[racon::Polisher::initialize] aligning overlaps [====================] 4.301526 s
[racon::Polisher::initialize] transformed data into windows 0.978941 s
[racon::Polisher::polish] generating consensus [====================] 0.563739 s
[racon::Polisher::] total = 17.828767 s
rvaser commented 2 years ago

Do you have a fastQ file? If so, what is the average quality score?

gettl008 commented 2 years ago

This is a published read set I pulled from NCBI and appears to be missing all quality info. No idea why...

rvaser commented 2 years ago

Could you provide the data for this example?