[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 1530449 sequences (154575349 bp)...
[main] Version: 0.7.5a-r405
[main] CMD: bwa mem -t 60 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bwa-indexes/hg38-no-haps.fa /oak/stanford/groups/akundaje/marinovg/papers/2024_Hi-KAS/2024-04-21-figures/juicer-GM12878-Rad21-ChIA-PET-ENCSR752QCX/splits/GM12878-Rad21-ChIA-PET-ENCSR752QCX_R1.fastq.gz
[main] Real time: 7881.671 sec; CPU: 75837.935 sec
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 5940596 sequences (600000196 bp)...
[M::main_mem] read 1530449 sequences (154575349 bp)...
[main] Version: 0.7.5a-r405
[main] CMD: bwa mem -t 60 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bwa-indexes/hg38-no-haps.fa /oak/stanford/groups/akundaje/marinovg/papers/2024_Hi-KAS/2024-04-21-figures/juicer-GM12878-Rad21-ChIA-PET-ENCSR752QCX/splits/GM12878-Rad21-ChIA-PET-ENCSR752QCX_R2.fastq.gz
[main] Real time: 7991.026 sec; CPU: 78780.547 sec
Picked up _JAVA_OPTIONS: -Xmx16384m
Picked up _JAVA_OPTIONS: -Xmx16384m
Picked up _JAVA_OPTIONS: -Xmx16384m
Picked up _JAVA_OPTIONS: -Xmx16384m
Picked up _JAVA_OPTIONS: -Xmx16384m
Warning: Hi-C map is too sparse to find many domains via Arrowhead.
Exiting. To disable sparsity check, use the --ignore_sparsity flag.