juicebox format to fasta: coordinates conversion error
Abby Bryson
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
