Settings:
  Output files: "gmac_GCF_031168955.1_ASM3116895v1.*.ht2"
  Line rate: 7 (line is 128 bytes)
  Lines per side: 1 (side is 128 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /gscratch/srlab/sam/data/G_macrocephalus/genomes/GCF_031168955.1_ASM3116895v1_genomic.fna
Reading reference sizes
  Time reading reference sizes: 00:00:05
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:04
  Time to read SNPs and splice sites: 00:00:02
Generation 0 (555444193 -> 555444193 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 1 (555668541 -> 555668541 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 2 (556117282 -> 556117282 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 3 (557014927 -> 557014927 nodes, 0 ranks)
BUILT FROM_INDEX: 2
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 1
RESIZE NODES: 7
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
1 14915218
2 17661883
6 27128776
3 19849916
6 18692184
2 16408669
6 16914113
2 20547161
38 23460273
2 20211512
6 17978261
2 13273088
7 12625219
7 21269883
2 18642488
38 15900337
2 17476677
6 14700810
2 11813362
6 14911255
2 16361017
6 13611779
1 13439169
38 18716760
2 12560394
1 9768105
5 10033351
2 12163144
1 11206146
5 10001527
1 8106621
1 9043324
1 16377403
5 9505541
1 8800849
1 9912942
1 14822425
2 1
16 1
128 2
FINISHED RECURSIVE SORTS: 2
SORT NODES: 3
MERGE, UPDATE RANK: 9
Generation 4 (558811586 -> 557941980 nodes, 347556972 ranks)
ALLOCATE FROM_TABLE: 5
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14759126
7 14772718
7 14745663
7 14737331
7 14774146
7 14774807
7 14720773
7 14732450
7 14767597
7 14742264
7 14770194
7 14740041
7 14759764
7 14773215
7 14746192
7 14777237
7 14720949
7 14759510
7 14770194
7 14746784
7 14725829
7 14781003
7 14748260
7 14755774
7 14750888
6 12649574
6 12620405
6 12645975
6 12629335
6 12652323
6 12648305
6 12634640
6 12644196
6 12620081
6 12654507
6 12651431
6 12643069
6 12645601
6 12635635
6 12114194
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 3
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 10
TOTAL TIME: 21
Generation 5 (558559987 -> 557905527 nodes, 447173183 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14758030
7 14771122
7 14744909
7 14737716
7 14771796
7 14773982
7 14721445
7 14735788
7 14765399
7 14742090
7 14768775
7 14740458
7 14757487
7 14771438
7 14745092
7 14773901
7 14720951
7 14758015
7 14766986
7 14745729
7 14725867
7 14778409
7 14746406
7 14753292
7 14749373
6 12647426
6 12622340
6 12644795
6 12628677
6 12652413
6 12647176
6 12634047
6 12642799
6 12620749
6 12652365
6 12650270
6 12643746
6 12644524
6 12635789
6 12113955
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 7
TOTAL TIME: 12
Generation 6 (558059915 -> 557997756 nodes, 488033829 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14761096
7 14773278
7 14747326
7 14741408
7 14773355
7 14777410
7 14724300
7 14740849
7 14767370
7 14744872
7 14771623
7 14743458
7 14758604
7 14773841
7 14747689
7 14775494
7 14723313
7 14759704
7 14768200
7 14747941
7 14728786
7 14780038
7 14747959
7 14754269
7 14751516
6 12648376
6 12626629
6 12646296
6 12630264
6 12655267
6 12648904
6 12636637
6 12644668
6 12622934
6 12653363
6 12652670
6 12646687
6 12646484
6 12638561
6 12116317
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 7
TOTAL TIME: 12
Generation 7 (558138390 -> 558077038 nodes, 520901965 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14764313
7 14774935
7 14749796
7 14745047
7 14774377
7 14779531
7 14727239
7 14744303
7 14768591
7 14746887
7 14773022
7 14745798
7 14759517
7 14775817
7 14750116
7 14776752
7 14725390
7 14760748
7 14769128
7 14749474
7 14731557
7 14781741
7 14749688
7 14754980
7 14753171
6 12649321
6 12630584
6 12647873
6 12632040
6 12657966
6 12650603
6 12639339
6 12646307
6 12625231
6 12653754
6 12654262
6 12649114
6 12648631
6 12641491
6 12118604
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 6
TOTAL TIME: 10
Generation 8 (558181901 -> 558131068 nodes, 539273927 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14765621
7 14776426
7 14751418
7 14748369
7 14774849
7 14779846
7 14729040
7 14746005
7 14769271
7 14747744
7 14774151
7 14746981
7 14760113
7 14777281
7 14752088
7 14777757
7 14727198
7 14761369
7 14770109
7 14750844
7 14734388
7 14782155
7 14751513
7 14755771
7 14754506
6 12650097
6 12634476
6 12648719
6 12633708
6 12659845
6 12652415
6 12640898
6 12646942
6 12625867
6 12653842
6 12655302
6 12650590
6 12649370
6 12643962
6 12120222
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 5
TOTAL TIME: 10
Generation 9 (558203646 -> 558163040 nodes, 549213118 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14766115
7 14777045
7 14752938
7 14750448
7 14775124
7 14779685
7 14729547
7 14746363
7 14769488
7 14748423
7 14775466
7 14747909
7 14760544
7 14778519
7 14753308
7 14778496
7 14728332
7 14761494
7 14770334
7 14751600
7 14736365
7 14781828
7 14753411
7 14756353
7 14755395
6 12650805
6 12637875
6 12648767
6 12634784
6 12661765
6 12653047
6 12640757
6 12647535
6 12626481
6 12653904
6 12655656
6 12651157
6 12649224
6 12645134
6 12121619
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 5
TOTAL TIME: 10
Generation 10 (558222058 -> 558190630 nodes, 553946345 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14766456
7 14777149
7 14753818
7 14753584
7 14775453
7 14779774
7 14730350
7 14746210
7 14770025
7 14749959
7 14777756
7 14748361
7 14761056
7 14780088
7 14754726
7 14778119
7 14729335
7 14761991
7 14770247
7 14751968
7 14736387
7 14781828
7 14756126
7 14755985
7 14756496
6 12651375
6 12639645
6 12648767
6 12635924
6 12662755
6 12652909
6 12640394
6 12648365
6 12627382
6 12653904
6 12655700
6 12650603
6 12649310
6 12645474
6 12124876
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 5
TOTAL TIME: 10
Generation 11 (558246671 -> 558220698 nodes, 556303271 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14767460
7 14776729
7 14754037
7 14758370
7 14775453
7 14779774
7 14730509
7 14746268
7 14770612
7 14751358
7 14779969
7 14749495
7 14761104
7 14782092
7 14755843
7 14778119
7 14730417
7 14762104
7 14770247
7 14752358
7 14735019
7 14781659
7 14760115
7 14755985
7 14758441
6 12651200
6 12641783
6 12648767
6 12637972
6 12663085
6 12652329
6 12641418
6 12649148
6 12629430
6 12653904
6 12655700
6 12650338
6 12649310
6 12645570
6 12127207
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 5
TOTAL TIME: 9
Generation 12 (558257399 -> 558233138 nodes, 557538929 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
7 14768515
7 14775815
7 14754176
7 14760447
7 14775377
7 14779774
7 14730509
7 14746483
7 14770051
7 14751358
7 14780012
7 14748864
7 14761104
7 14782092
7 14757750
7 14778119
7 14730417
7 14762104
7 14770247
7 14752358
7 14734818
7 14781659
7 14765242
7 14755985
7 14759058
6 12651022
6 12639330
6 12648767
6 12640171
6 12662812
6 12651726
6 12643162
6 12649148
6 12632116
6 12653904
6 12655700
6 12650338
6 12649310
6 12645494
6 12127804
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 3
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 5
TOTAL TIME: 10
Generation 13 (558242638 -> 558228626 nodes, 558074429 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14768515
7 14775815
7 14754176
7 14758715
7 14775377
7 14779774
7 14730509
7 14746483
7 14770051
7 14751358
7 14780270
7 14745420
7 14761104
7 14780774
7 14761846
7 14778119
7 14730417
7 14762104
7 14770247
7 14752358
7 14734818
7 14781659
7 14763092
7 14755985
7 14759058
6 12651022
6 12639330
6 12648767
6 12640547
6 12662387
6 12651726
6 12643162
6 12649148
6 12632116
6 12653904
6 12655700
6 12650338
6 12649310
6 12645494
6 12127631
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 5
TOTAL TIME: 10
Generation 14 (558232679 -> 558228771 nodes, 558221708 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14768515
7 14775815
7 14753734
7 14758715
7 14775377
7 14779774
7 14730509
7 14746483
7 14770051
7 14751358
7 14780270
7 14745420
7 14761104
7 14780774
7 14765689
7 14778119
7 14729069
7 14762104
7 14770247
7 14752358
7 14734818
7 14781659
7 14762794
7 14755985
7 14759058
6 12651022
6 12637720
6 12648767
6 12640547
6 12662387
6 12651726
6 12643162
6 12649148
6 12632116
6 12653904
6 12655700
6 12650338
6 12649310
6 12645494
6 12127631
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 5
TOTAL TIME: 9
Generation 15 (558228771 -> 558228771 nodes, 558228771 ranks)
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14768515
7 14775815
7 14753734
7 14758715
7 14775377
7 14779774
7 14730509
7 14746483
7 14770051
7 14751358
7 14780270
7 14745420
7 14761104
7 14780774
7 14765689
7 14778119
7 14729069
7 14762104
7 14770247
7 14752358
7 14734818
7 14781659
7 14762794
7 14755985
7 14759058
6 12651022
6 12637720
6 12648767
6 12640547
6 12662387
6 12651726
6 12643162
6 12649148
6 12632116
6 12653904
6 12655700
6 12650338
6 12649310
6 12645494
6 12127631
FINISHED RECURSIVE SORTS: 1
Generating edges... 
NODE.TO -> GENOME POS: 2
BUILD FROM_INDEX 2
COUNTED NEW EDGES: 0
MADE NEW EDGES: 3
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
6 4485735
6 4267918
6 4416036
8 4109354
7 4150120
7 3873558
9 4246912
7 4183740
7 4221587
6 3687231
7 3994651
3 3900093
5 4150689
6 3914173
6 3712384
8 3839676
7 3746959
7 3899163
9 3735519
7 3599210
6 3983847
5 4164202
6 3640930
6 3695443
7 4125559
6 3659858
7 3845214
7 3609744
10 3885383
6 3974508
6 3843872
6 3398700
8 3705229
8 3595047
7 3669374
7 3364091
7 3062036
6 2999525
6 3152449
6 2541046
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
7 3327114
7 3526712
7 3352920
3 4042189
5 3468702
5 3197299
5 3137802
6 3681513
6 3683055
6 3442370
6 3368419
6 3318763
6 3221711
8 3062911
7 3295382
7 3394335
5 3552803
6 3440808
6 3275098
6 2993411
6 3331484
6 3151892
12 3042636
10 2956693
9 3052927
10 3030128
10 3164388
12 3193989
7 2983321
8 3088291
6 3466649
5 3205176
4 3278276
6 3099939
5 3025804
5 2720588
8 2482850
6 2769529
6 2385290
6 2116231
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
8 3213486
7 3393810
10 3226397
7 3225755
7 3435210
4 3215374
6 3466291
6 3206562
9 3509805
8 3297658
10 3191883
7 3291738
8 3444125
7 3137196
7 3134210
6 3235559
8 3301444
7 3404950
7 3424587
6 3420101
7 3317146
6 3330376
6 3199080
6 3350757
5 3442490
7 3447013
8 3045580
7 3063324
7 3204851
8 3318638
7 3168452
7 3071139
6 2845359
6 3232677
5 4542470
3 2480057
6 2554183
5 2290437
5 2272572
5 1943789
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
9 4197225
9 3907439
10 3794551
10 4186712
12 4065201
9 4468215
8 3742916
6 3786690
9 3831517
8 4052459
7 3993436
8 4189610
7 3757581
8 4135273
5 4013438
6 3756183
6 4087036
7 3783073
6 4152601
6 3742177
6 3898784
6 3693892
7 3964980
5 4024225
5 3838498
4 5369233
4 3450054
5 3552165
6 3522616
6 3925433
6 3593742
7 3414193
6 3412793
7 3470338
9 3748565
5 3662250
5 3520381
4 2835418
4 2744943
4 2491179
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 5
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
7 14680064
6 12582912
6 12582912
6 12582912
6 12582912
6 12582912
6 12582912
6 12582912
6 12582912
6 12582912
6 12582912
6 12582912
6 12582912
6 10872099
FINISHED RECURSIVE SORTS: 1
RE-SORTED NODES: 5
PROCESS EDGES: 2
REMOVE Y: 1
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
7 14680731
7 14681418
7 14681075
7 14682275
7 14693887
7 14688005
7 14698132
7 14694753
7 14681452
7 14681521
7 14682000
7 14684956
7 14697933
7 14688786
7 14690327
7 14701551
7 14686119
7 14691797
7 14701753
7 14684665
7 14684495
7 14684529
7 14684685
7 14687360
7 14688240
7 14685035
7 14683362
6 12585312
6 12584442
6 12583835
6 12584524
6 12583927
6 12584014
6 12583975
6 12584168
6 12583829
6 12583621
6 12583970
6 12584259
6 10872992
FINISHED RECURSIVE SORTS: 1
SORT, Make index: 6
TOTAL: 26
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 152050765
fchr[G]: 279380163
fchr[T]: 406676694
fchr[$]: 558453709
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 347918103 bytes to primary GFM file: gmac_GCF_031168955.1_ASM3116895v1.1.ht2
Wrote 139557200 bytes to secondary GFM file: gmac_GCF_031168955.1_ASM3116895v1.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 376924113 bytes to primary GFM file: gmac_GCF_031168955.1_ASM3116895v1.5.ht2
Wrote 141646948 bytes to secondary GFM file: gmac_GCF_031168955.1_ASM3116895v1.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt constructor
Headers:
    len: 555215489
    gbwtLen: 558453710
    nodes: 558228770
    sz: 277607745
    gbwtSz: 279226856
    lineRate: 7
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 34889299
    offsSz: 139557196
    lineSz: 128
    sideSz: 128
    sideGbwtSz: 104
    sideGbwtLen: 208
    numSides: 2684874
    numLines: 2684874
    gbwtTotLen: 343663872
    gbwtTotSz: 343663872
    reverse: 0
    linearFM: No
Total time for call to driver() for forward index: 00:08:44