hicpro2juicebox.sh: allValidPairs.pre_juicebox_sorted does not exist or does not contain any reads

[TheRaspberryFox]

Hello, I have ran HiC-Pro and generated my validpairs file. I am currently trying to convert it to a .hic file. However, I keep running into this error where "allValidPairs.pre_juicebox_sorted does not exist or does not contain any reads". I am struggling to figure out the reason for this occurring.

Here is the current error message:

HiC-Pro format > 2.7.5 detected ...
Generating Juicebox input files ...
/software/hic-pro/3.1.0/HiC-Pro/bin/utils/hicpro2juicebox.sh: line 142: 72618 Done
awk '{$4=$4!="+"; $7=$7!="+"; n1=split($9, frag1, "_"); n2=split($10, frag2, "_"); } $2<=$5{print $1, $4, $2, $3, frag1[n1], $7, $5, $6, frag2[n2], $11, $12 }$5<$2{ print $1, $7, $5, $6, frag2[n2], $4, $2, $3, frag1[n1], $12, $11}' $VALIDPAIRS
72619 Killed | LANG=C sort -T ${TEMP} -k3,3d -k7,7d -S 50% --parallel=4 > ${TEMP}/$$_allValidPairs.pre_juicebox_sorted
Running Juicebox ...
WARN [2024-01-24T12:04:10,890]  [Globals.java:138] [main]  Development mode is enabled
Using 1 CPU thread(s)
./tmp/71130_allValidPairs.pre_juicebox_sorted does not exist or does not contain any reads.
done !

[nservant]

I think this is a sort issue ... my guess is that it did not finish