Error generating HIC map with juicer tools pre - ArrayIndexOutOfBoundsException

[Lorenzo Bertola]

Hello,

I am trying to generate input files for manual curation of an assembly in Juicebox.

I have 3 input files per haplotype: agp output of YAHS, bam file of HIC reads, and indexed contigs fasta file used as input for YAHS.

I run the following commands:

`yahs/juicer pre Hap2_HIC.bam Hap2_YAHS.agp Hap2_Contigs.fasta.fai | sort -k2,2d -k6,6d -T ./ | awk 'NF' > alignments_sorted_v2.txt`

`java -jar -Xmx64G juicer_tools.jar pre alignments_sorted_v2.txt out_v2.hic Hap2_ChromSize.txt`

The juicer_tools.jar version is that provided with YAHS, v.1.9.9.

These commands work fine for Haplotype 1, and I am able to proceed onto the next steps with no issues.

For Haplotype 2 although I get the following error:

Below are comparisons of the input files for Hap1 and Hap2

AGP output from YAHS

samtools faidx index of contigs.fasta file used as input for YAHS

alignment_sorted file produced with yahs/juicer pre

HIC bam files used as input for YAHS

ChromSize files. (Note that for Hap2 two chromosomes were joined into one scaffold, hence the apparent difference in size)

Any suggestion as to what might be causing this would be highly appreciated

Cheers,
Lorenzo

[Olga Dudchenko]

JBAT will only work with .assembly style files. I understand YAHS people have a converter, but generally speaking you can always visualize whatever assembly you want with 3D-DNA which is part of the same suite. See Genome Assembly Cookbook (dnazoo.org/methods) for instructions. Best, -Olga