[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 15789474 sequences (600000012 bp)...
[M::mem_process_seqs] Processed 15789474 reads in 1893.453 CPU sec, 268.649 real sec
[M::process] read 15789474 sequences (600000012 bp)...
[M::mem_process_seqs] Processed 15789474 reads in 1478.087 CPU sec, 151.633 real sec
[M::process] read 15789474 sequences (600000012 bp)...
[M::mem_process_seqs] Processed 15789474 reads in 1205.383 CPU sec, 77.027 real sec
[M::process] read 15789474 sequences (600000012 bp)...
[M::mem_process_seqs] Processed 15789474 reads in 1200.949 CPU sec, 76.728 real sec
[M::process] read 8870974 sequences (337097012 bp)...
[M::mem_process_seqs] Processed 8870974 reads in 669.131 CPU sec, 42.690 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 60 /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-03-10-NextSeq-run/final-post-review-merge_debris_50kb/bwa-indexes/symbB.v1.0.genome.FINAL.merge_debris_50kb.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2020-06-12-NextSeq-run/juicer-L1521-Symbiodinium_48h_a-amanitin-Hi-C-symbB.v1.0.genome.FINAL-final-post-review-merge_debris_50kb-all_reads/splits/L1521-Symbiodinium_48h_a-amanitin-Hi-C_R1.fastq.gz
[main] Real time: 845.130 sec; CPU: 6638.218 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 15789474 sequences (600000012 bp)...
[M::mem_process_seqs] Processed 15789474 reads in 1926.320 CPU sec, 275.424 real sec
[M::process] read 15789474 sequences (600000012 bp)...
[M::mem_process_seqs] Processed 15789474 reads in 1476.824 CPU sec, 149.630 real sec
[M::process] read 15789474 sequences (600000012 bp)...
[M::mem_process_seqs] Processed 15789474 reads in 1216.669 CPU sec, 78.234 real sec
[M::process] read 15789474 sequences (600000012 bp)...
[M::mem_process_seqs] Processed 15789474 reads in 1216.453 CPU sec, 77.504 real sec
[M::process] read 8870974 sequences (337097012 bp)...
[M::mem_process_seqs] Processed 8870974 reads in 677.130 CPU sec, 43.114 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 60 /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-03-10-NextSeq-run/final-post-review-merge_debris_50kb/bwa-indexes/symbB.v1.0.genome.FINAL.merge_debris_50kb.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/DNAzoo/2020-06-12-NextSeq-run/juicer-L1521-Symbiodinium_48h_a-amanitin-Hi-C-symbB.v1.0.genome.FINAL-final-post-review-merge_debris_50kb-all_reads/splits/L1521-Symbiodinium_48h_a-amanitin-Hi-C_R2.fastq.gz
[main] Real time: 868.409 sec; CPU: 6709.477 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.