integration with juicer

[Overcraft90]

Hi there,

I was working with RagTag to correct and scaffold the genome of a plant species based on the reference. Everything works just fine; however, I wish to generate contact maps with juicertools.

The first step requires a BIN/BAM which for YaSH, at least the BIN, is a standard output file — for RagTag I'm using the BAM alignment from Hi-C to the assembly I'm scaffolding, the AGP which also RagTag outputs as file format, and a FAI index which is the one for the reference genome.

Everything seems to work properly but then the TXT file in output from the command below is empty...

juicer pre -a -o $d/${ID}_${HAP}_JBAT ${ID}.${HAP}.bam $d/${ID}_${HAP}_ragtag-2/ragtag.scaffold.agp ../INLUP_amiga.fa.fai > $d/${ID}_${HAP}_JBAT.log 2>&1

Does anyone have any recommendation, or experience, in working with the combination of these two tools so that I can figure out what is going wrong? Also, there seems to be not many issues on this on the juicer Git page but if helpful I will ask there, too.