[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 2099994 sequences (314999100 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/ENCODE4/Chromatin-nanopores/2022-01-22-Novogene-OS-NovaSeq/juicer-L2258-OS89_Hi-C/splits/L2258-OS89_Hi-C_R1.fastq.gz
[main] Real time: 12478.441 sec; CPU: 172057.065 sec
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 4000000 sequences (600000000 bp)...
[M::main_mem] read 2099994 sequences (314999100 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/ENCODE4/Chromatin-nanopores/2022-01-22-Novogene-OS-NovaSeq/juicer-L2258-OS89_Hi-C/splits/L2258-OS89_Hi-C_R2.fastq.gz
[main] Real time: 12942.705 sec; CPU: 178782.947 sec
Picked up _JAVA_OPTIONS: -Xmx16384m
Iterated 1000 times, returning estimate
Picked up _JAVA_OPTIONS: -Xmx16384m
Picked up _JAVA_OPTIONS: -Xmx16384m
Iterated 1000 times, returning estimate
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.