[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 8757094 sequences (332769572 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/Symbiodinium/2021-05-29-NextSeq-run/juicer-L2117-PSS0141-Hi-C/splits/L2117-PSS0141-Hi-C_R1.fastq.gz
[main] Real time: 27645.070 sec; CPU: 364182.070 sec
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 15789474 sequences (600000012 bp)...
[M::main_mem] read 8757094 sequences (332769572 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/Symbiodinium/2021-05-29-NextSeq-run/juicer-L2117-PSS0141-Hi-C/splits/L2117-PSS0141-Hi-C_R2.fastq.gz
[main] Real time: 28518.107 sec; CPU: 378096.471 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.