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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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juicebox format to fasta: coordinates conversion error #336

Closed brysonab closed 1 year ago

brysonab commented 1 year ago

Hi Juicer Team!

I am working with a large plant genome, around 3Gbp. I am having an issue converting the assembly from the reviewed version in Juicebox to fasta format.

The .agp file seems to be correct: (first 3 lines) ctg00000001.1 1 2037903 1 W contig_4076_pilon 1 2037903 + ctg00000002.1 1 144558 1 W contig_11429_pilon 1 144558 + ctg00000003.1 1 11901176 1 W contig_4092_pilon 1 11901176 +

Here is my command: juicer post -o out_JBAT_final pilon_out.review.assembly out_JBAT.liftover.agp draft_contigs.fasta

And here is the error: [E::assembly_to_agp] coordinates conversion error contig_16500_pilon 0

I am wondering if it may have something to do with the scale. Because it is large, the scale should be 2.0 and I set it in Juicebox. Any thoughts would be greatly appreciated! -Abby

sa501428 commented 1 year ago

Hi! This would actually be more of a 3D-DNA question / should be posted to the forum: https://groups.google.com/g/3d-genomics