[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/hg20/bwa-indexes/hg38-no-haps.fa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ssDNA/2020-12-18-NextSeq-run/juicer-L1971-L1972-L1973-L11974-GM12878_HiKAS_10M/splits/L1971-L1972-L1973-L11974-GM12878_HiKAS_10M_R1.fastq.gz
[main] Real time: 26171.242 sec; CPU: 212188.232 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/hg20/bwa-indexes/hg38-no-haps.fa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ssDNA/2020-12-18-NextSeq-run/juicer-L1971-L1972-L1973-L11974-GM12878_HiKAS_10M/splits/L1971-L1972-L1973-L11974-GM12878_HiKAS_10M_R2.fastq.gz
[main] Real time: 28764.424 sec; CPU: 222835.836 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.