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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
271 stars 49 forks source link

chimeric in window #87

Closed njaupan closed 6 years ago

njaupan commented 6 years ago

Dear Ivan, I have used the command below for a draft genome that is 130x coverage assembled by smartdenovo, ~bin/racon -t 12 reads reads2fasta.minimap2.sam fasta -w 1500 > racon.fa and meet error like this: [racon::Window::generate_consensus] warning: contig 0 might be chimeric in window 3!

Do you have any suggestions?

Best, panpan

rvaser commented 6 years ago

Hello, this message is just a warning from a postprocessing heuristic step which indicates that the printed contig might be chimeric. You can ignore the message as the heuristic has not been tested intensively.

Best regards, Robert

jtoy7 commented 2 years ago

Hi Robert,

I see this thread was from a few years back, but I am getting the same warning. Is it still okay to ignore the message? I am running v1.4.13

[racon::Window::generate_consensus] warning: contig 398 might be chimeric in window 2!

Thanks, Jason

rvaser commented 2 years ago

Hi Jason, yes you can ignore it.

Best regards, Robert

jtoy7 commented 2 years ago

Great, thanks!

emily-ap commented 2 months ago

hello, checking in to make sure it's still okay to ignore this since it's been a few years. Thanks!