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sanger-pathogens / circlator

A tool to circularize genome assemblies
http://sanger-pathogens.github.io/circlator/
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circlator failed to detect Canu 'suggestCircular=yes' contigs #161

Open bitcometz opened 4 years ago

bitcometz commented 4 years ago

Hello,

I used the canu + Polish + circlator to assembly bacterial genomes. The largest contig in canu assembly is considered as 'suggestCircular'. But in the circlator :

[merge circularise_details] tig00000001|arrow Checking 8 nucmer hits [merge circularise_details] tig00000001|arrow potential pair of nucmer hits for circularization: [merge circularise_details] tig00000001|arrow 1 12322 29044 41367 12322 12324 97.11 4417207 76689 1 tig00000001|arrow NODE_4_length_76689_cov_22.460131 [merge circularise_details] tig00000001|arrow 4367209 4408566 1 41367 41358 41367 99.17 4417207 76689 1 tig00000001|arrow NODE_4_length_76689_cov_22.460131 [merge circularise_details] tig00000001|arrow cannot use this pair because longer match was found [merge circularise_details] tig00000001|arrow cannot use this pair because positions/orientations of matches no good [merge circularise_details] tig00000001|arrow Trying to circularize. Has nucmer hits to check... [merge circularise_details] tig00000001|arrow No matches to SPAdes circular contigs [merge circularise_details] tig00000001|arrow Could not circularize using matches to spades circular contigs [merge circularise_details] tig00000001|arrow Cannot circularize: no suitable nucmer hits [merge circularise_details] tig00000001|arrow Circularized: no

How can I optimize the parameters for circlator to consider this contig as Circularized?

Thanks!!!!

rthapa1 commented 3 years ago

Hi, were you able to fix this?

minhtrung1997 commented 1 year ago

I have the same issue with Flye