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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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Racon cannot work with duplucates in paf file #233

Open Oieswarya opened 1 year ago

Oieswarya commented 1 year ago

I have aligned contigs to longreads using Minimap2 and generated the paf file. I am trying to use racon to get a consensus of these. The command I am using: ./racon PA_hifi.fa minimapConToHiFimapped_PA.paf minia_contigs_Pseudomonas.contigs.fa

and the error I am getting is: [racon::Polisher::initialize] loaded target sequences 0.059568 s [racon::Polisher::initialize] error: duplicate sequence 0 with unequal data

I know that minimap2 gives more than one position for a particular contig. Is that the reason I am getting this error?

But I am also having the same error with mashmap alignment where it is giving me one hit. I have checked by grep if my files have any duplicate sequences or not which it does not.

rvaser commented 1 year ago

Hello, do files PA_hifi.fa and minia_contigs_Pseudomonas.contigs.fa have a sequence with the same name but different data? Racon has error correction mode for which we included a check that if a sequence name appears in both files it should have the same length (which should imply the same contents).

Best regards, Robert