1580 regions [M::mm_idx_gen::9.432*1.59] collected minimizers [M::mm_idx_gen::12.020*2.00] sorted minimizers [M::main::12.020*2.00] loaded/built the index for 10 target sequence(s) [M::mm_mapopt_update::13.108*1.92] mid_occ = 348 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 10 [M::mm_idx_stat::13.748*1.87] distinct minimizers: 77597414 (86.16% are singletons); average occurrences: 1.861; average spacing: 5.468; total length: 789630056 [M::worker_pipeline::13.919*1.91] mapped 305 sequences [M::main] Version: 2.30-r1287 [M::main] CMD: minimap2 -c -x asm20 -t 8 data/13-wgbs-genome-hapa/Och_HapA_assembly.fa output/13-wgbs-hapa/13.10-compare/query_long.fa [M::main] Real time: 14.065 sec; CPU: 26.672 sec; Peak RSS: 3.997 GB [M::mm_idx_gen::9.105*1.55] collected minimizers [M::mm_idx_gen::10.635*2.09] sorted minimizers [M::main::10.635*2.09] loaded/built the index for 10 target sequence(s) [M::mm_mapopt_update::10.635*2.09] mid_occ = 1000 [M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 10 [M::mm_idx_stat::11.299*2.03] distinct minimizers: 75083900 (87.66% are singletons); average occurrences: 1.766; average spacing: 5.957; total length: 789630056 [M::worker_pipeline::11.399*2.04] mapped 1275 sequences [M::main] Version: 2.30-r1287 [M::main] CMD: minimap2 -c -x sr -t 8 data/13-wgbs-genome-hapa/Och_HapA_assembly.fa output/13-wgbs-hapa/13.10-compare/query_dml.fa [M::main] Real time: 11.521 sec; CPU: 23.377 sec; Peak RSS: 3.803 GB QC (merged -> HapA), mean over oysters: mapping_pct 57.4 -> 67.4 multimap_pct 31.9 -> 15.8 cpgs_5x 7,862,777.7 -> 9,129,882.7 Shared chromosomes (2A/4A/6A/10A, identical in both): Pum1 CpGs>=5x both 3,457,072 depth ratio 1.063 r 0.9954 mean |diff| 0.71% Qui1 CpGs>=5x both 3,634,727 depth ratio 1.062 r 0.9953 mean |diff| 0.69% Qui2 CpGs>=5x both 3,136,059 depth ratio 1.062 r 0.9953 mean |diff| 0.76% Qui3 CpGs>=5x both 3,663,625 depth ratio 1.062 r 0.9953 mean |diff| 0.72% Qui4 CpGs>=5x both 3,196,595 depth ratio 1.062 r 0.9953 mean |diff| 0.69% Rio1 CpGs>=5x both 3,922,014 depth ratio 1.057 r 0.9954 mean |diff| 0.7% Rio2 CpGs>=5x both 3,321,874 depth ratio 1.06 r 0.9954 mean |diff| 0.69% Rio3 CpGs>=5x both 2,806,089 depth ratio 1.06 r 0.9954 mean |diff| 0.73% Rio4 CpGs>=5x both 3,772,012 depth ratio 1.061 r 0.9954 mean |diff| 0.71% DMR windows: 304 regions lift to HapA: ok 290, unmapped 11, < 50% of query aligned 3 class n both same sign replicated r no genetic signal 82 80 77 (96%) 75 (94%) 0.94 untested 125 117 114 (97%) 107 (91%) 0.95 genetic: CpG-destroying 41 37 26 (70%) 21 (57%) 0.75 repeat-like 36 36 34 (94%) 28 (78%) 0.89 genetic: other 20 19 19 (100%) 17 (89%) 0.96 (both = measurable on both references; replicated = same sign and |HapA diff| >= 10%) DML CpGs: 1275 regions lift to HapA: ok 1099, no CpG on HapA 129, unmapped 38, CpG in an indel 9 class n both same sign replicated r no genetic signal 488 461 450 (98%) 425 (92%) 0.97 untested 333 301 296 (98%) 279 (93%) 0.97 genetic: CpG-destroying 204 102 93 (91%) 90 (88%) 0.91 repeat-like 149 135 125 (93%) 104 (77%) 0.89 genetic: other 101 81 80 (99%) 78 (96%) 0.97 (both = measurable on both references; replicated = same sign and |HapA diff| >= 20%) GN020540 -> Chromosome_9A:61735450-61741949 (-), identity 1.000, query covered 1.00 Pum1 merged 36.9% (1555 calls) HapA 35.2% (1640 calls) Qui1 merged 61.1% (1383 calls) HapA 61.2% (1416 calls) Qui2 merged 37.1% (1352 calls) HapA 36.2% (1407 calls) Qui3 merged 35.7% (1802 calls) HapA 34.3% (1893 calls) Qui4 merged 40.5% (1105 calls) HapA 39.6% (1135 calls) Rio1 merged 2.7% (1463 calls) HapA 2.7% (1465 calls) Rio2 merged 2.3% (1237 calls) HapA 2.7% (1276 calls) Rio3 merged 4.3% ( 986 calls) HapA 4.5% (1032 calls) Rio4 merged 3.4% (1405 calls) HapA 3.9% (1449 calls)