[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 469114 sequences (35652664 bp)...
[main] Version: 0.7.5a-r405
[main] CMD: bwa mem -t 60 /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bwa-indexes/hg19-male.fa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ssDNA/2021-01-13-GM18278-hg19-reprocessing/juicer-L1971-L1972-L1973-L11974-GM12878_HiKAS_10M-hg19/splits/L1971-L1972-L1973-L11974-GM12878_HiKAS_10M_R1.fastq.gz
[main] Real time: 18939.651 sec; CPU: 155044.233 sec
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 7894738 sequences (600000088 bp)...
[M::main_mem] read 469114 sequences (35652664 bp)...
[main] Version: 0.7.5a-r405
[main] CMD: bwa mem -t 60 /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bwa-indexes/hg19-male.fa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ssDNA/2021-01-13-GM18278-hg19-reprocessing/juicer-L1971-L1972-L1973-L11974-GM12878_HiKAS_10M-hg19/splits/L1971-L1972-L1973-L11974-GM12878_HiKAS_10M_R2.fastq.gz
[main] Real time: 19625.105 sec; CPU: 162103.180 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.