Settings:
  Output files: "../data/Phel_genome_index.*.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:
  ../data/ncbi_dataset/data/GCA_032158295.1/GCA_032158295.1_ASM3215829v1_genomic.fna
Reading reference sizes
  Time reading reference sizes: 00:00:04
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:02
  Time to read SNPs and splice sites: 00:00:00
Generation 0 (483954537 -> 483954537 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 4
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 1 (484091882 -> 484091882 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 4
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 2 (484366576 -> 484366576 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 4
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 3 (484916235 -> 484916235 nodes, 0 ranks)
BUILT FROM_INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 4
RESIZED NODES: 0
MADE NEW NODES: 0
RESIZE NODES: 9
COUNT NUMBER IN EACH BIN: 2
FINISHED FIRST ROUND: 1
1 20886481
2 18541998
1 13450972
6 17607185
7 19338561
3 18874522
6 16395122
2 22809817
37 11834372
2 14101746
6 16604742
3 13841603
8 11896647
6 10833993
2 16050321
38 14419491
2 12261219
6 10768227
7 13214151
2 9608421
6 13043865
2 12290907
1 9544450
37 11052424
2 12402289
1 9612820
5 9839027
2 8827425
6 17838453
2 13865641
1 11553772
5 11049837
1 9083898
1 11806443
1 20868262
0 0
0 0
18 1
38 1
90 1
FINISHED RECURSIVE SORTS: 2
SORT NODES: 5
MERGE, UPDATE RANK: 7
Generation 4 (486019107 -> 485458925 nodes, 302048258 ranks)
ALLOCATE FROM_TABLE: 7
COUNT NUMBER IN EACH BIN: 2
FINISHED FIRST ROUND: 2
12 12626788
12 12632706
12 12628023
12 12631175
12 12626868
12 12629173
12 12626639
12 12623297
12 12628994
12 12630874
12 12626092
12 12623001
12 12623885
12 12629997
12 12632126
12 12632981
12 12629590
12 12630274
12 12617405
12 12621430
12 12629230
12 12630990
11 11572832
11 11572479
11 11566081
11 11573110
11 11571771
11 11573460
11 11568878
11 11575836
11 11590711
11 11585759
11 11574517
11 11573318
11 11579542
11 11583954
11 11585035
11 11556348
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 5
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 6
TOTAL TIME: 22
Generation 5 (485743916 -> 485449217 nodes, 413824412 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
12 12625942
12 12631503
12 12627466
12 12631204
12 12626481
12 12630283
12 12626346
12 12623635
12 12628416
12 12630495
12 12625511
12 12622565
12 12623324
12 12629289
12 12631354
12 12631833
12 12628500
12 12629797
12 12617420
12 12621033
12 12628745
12 12632256
11 11571921
11 11572164
11 11566434
11 11572951
11 11571935
11 11573816
11 11570130
11 11575035
11 11591002
11 11585652
11 11573549
11 11572546
11 11579663
11 11583796
11 11585076
11 11556393
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 3
TOTAL TIME: 10
Generation 6 (485531740 -> 485501772 nodes, 446361247 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
12 12626453
12 12632314
12 12628486
12 12633135
12 12628084
12 12633168
12 12627518
12 12625572
12 12629764
12 12631964
12 12627082
12 12623815
12 12624246
12 12630467
12 12632547
12 12632867
12 12629217
12 12631083
12 12618893
12 12622229
12 12629955
12 12634960
11 11572710
11 11573195
11 11567929
11 11573906
11 11573166
11 11576235
11 11572622
11 11575903
11 11592949
11 11587007
11 11574060
11 11573050
11 11581608
11 11585661
11 11586996
11 11557200
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 2
TOTAL TIME: 10
Generation 7 (485581103 -> 485555156 nodes, 466019828 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
12 12626860
12 12633038
12 12629530
12 12635510
12 12629575
12 12635993
12 12628630
12 12627858
12 12631422
12 12633724
12 12629237
12 12625042
12 12624951
12 12631462
12 12633646
12 12633819
12 12630303
12 12632279
12 12620130
12 12623953
12 12631486
12 12637763
11 11573643
11 11573950
11 11569262
11 11574748
11 11574138
11 11579041
11 11574851
11 11576735
11 11595012
11 11588214
11 11574696
11 11573505
11 11583342
11 11587397
11 11588574
11 11558081
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 2
TOTAL TIME: 10
Generation 8 (485630748 -> 485608794 nodes, 475515427 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
12 12627101
12 12633656
12 12630467
12 12638165
12 12630879
12 12638547
12 12629590
12 12629896
12 12632752
12 12635433
12 12631405
12 12626163
12 12625442
12 12632550
12 12633993
12 12635157
12 12631636
12 12633383
12 12621908
12 12626004
12 12633049
12 12640396
11 11574502
11 11574813
11 11570550
11 11575068
11 11574929
11 11582407
11 11576891
11 11577692
11 11597142
11 11589506
11 11575505
11 11574099
11 11585480
11 11589484
11 11590201
11 11559197
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 4
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 2
TOTAL TIME: 9
Generation 9 (485687999 -> 485665025 nodes, 480521691 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
12 12627450
12 12634304
12 12631067
12 12641335
12 12631744
12 12640265
12 12630799
12 12631755
12 12632823
12 12637586
12 12634216
12 12626882
12 12626145
12 12634319
12 12634535
12 12636604
12 12632892
12 12634354
12 12622598
12 12627977
12 12634644
12 12643907
11 11575832
11 11576297
11 11571987
11 11575529
11 11575904
11 11585735
11 11578836
11 11579083
11 11598762
11 11590813
11 11576886
11 11575072
11 11587074
11 11592662
11 11591530
11 11561066
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 2
TOTAL TIME: 9
Generation 10 (485743525 -> 485717598 nodes, 483506537 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
12 12628474
12 12634300
12 12631134
12 12645785
12 12632380
12 12640502
12 12631700
12 12632875
12 12632688
12 12639232
12 12637585
12 12628189
12 12626511
12 12636472
12 12634545
12 12638062
12 12633276
12 12633473
12 12623016
12 12629986
12 12635339
12 12646551
11 11576874
11 11578381
11 11573110
11 11576496
11 11576996
11 11591219
11 11581516
11 11579955
11 11600658
11 11592427
11 11578381
11 11575651
11 11588862
11 11594710
11 11592515
11 11564016
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 2
TOTAL TIME: 10
Generation 11 (485783162 -> 485752837 nodes, 484990294 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
12 12628838
12 12633811
12 12630530
12 12649603
12 12633816
12 12639986
12 12629501
12 12632277
12 12632687
12 12642217
12 12639374
12 12630298
12 12625823
12 12637165
12 12634545
12 12636874
12 12633202
12 12632119
12 12624459
12 12631330
12 12635203
12 12646790
11 11577689
11 11579159
11 11573164
11 11576540
11 11578688
11 11599426
11 11582787
11 11581372
11 11602277
11 11593418
11 11580319
11 11575584
11 11590084
11 11596992
11 11593529
11 11567605
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 4
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 2
TOTAL TIME: 9
Generation 12 (485792697 -> 485766488 nodes, 485603335 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
12 12628838
12 12633811
12 12630249
12 12651722
12 12635119
12 12639634
12 12629501
12 12632046
12 12632615
12 12644216
12 12638895
12 12632100
12 12625575
12 12637441
12 12634545
12 12636653
12 12633202
12 12632119
12 12624822
12 12630336
12 12633772
12 12645635
11 11577686
11 11578738
11 11572509
11 11575467
11 11581144
11 11604379
11 11581930
11 11582302
11 11603188
11 11593429
11 11581262
11 11575255
11 11591029
11 11598848
11 11593190
11 11569530
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 1
TOTAL TIME: 9
Generation 13 (485772492 -> 485760846 nodes, 485753917 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
12 12627681
12 12633811
12 12630249
12 12651722
12 12635119
12 12639634
12 12629501
12 12632046
12 12632615
12 12644242
12 12638519
12 12632100
12 12625575
12 12634587
12 12634545
12 12636653
12 12633202
12 12632119
12 12624822
12 12630336
12 12633772
12 12645635
11 11577686
11 11578738
11 11572509
11 11575467
11 11581144
11 11603187
11 11581930
11 11582302
11 11603188
11 11593429
11 11581262
11 11575255
11 11590099
11 11599689
11 11593190
11 11569530
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 2
TOTAL TIME: 10
Generation 14 (485760846 -> 485760846 nodes, 485760846 ranks)
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
12 12627681
12 12633811
12 12630249
12 12651722
12 12635119
12 12639634
12 12629501
12 12632046
12 12632615
12 12644242
12 12638519
12 12632100
12 12625575
12 12634587
12 12634545
12 12636653
12 12633202
12 12632119
12 12624822
12 12630336
12 12633772
12 12645635
11 11577686
11 11578738
11 11572509
11 11575467
11 11581144
11 11603187
11 11581930
11 11582302
11 11603188
11 11593429
11 11581262
11 11575255
11 11590099
11 11599689
11 11593190
11 11569530
11 11534336
11 10909420
FINISHED RECURSIVE SORTS: 1
Generating edges... 
NODE.TO -> GENOME POS: 2
BUILD FROM_INDEX 1
COUNTED NEW EDGES: 1
MADE NEW EDGES: 4
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
9 3999639
10 4011189
9 3788629
10 3906056
9 3828363
10 3753830
11 3747072
11 3814078
11 3743862
11 3873982
10 3846815
11 3981371
11 3939107
11 3802238
11 3853193
11 3676948
11 3702126
13 3848361
13 3876132
12 3682082
12 3664569
12 3852538
12 3797936
12 3664350
12 3559760
12 3525603
13 3545980
13 3718358
12 3540030
12 3693986
12 3584815
13 3709762
13 3464733
13 3558766
13 3595598
13 3543385
12 3398349
13 3262122
12 3279284
13 3240831
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
11 2428473
11 2568045
10 2438372
10 2421337
11 2575674
10 2532465
10 2548574
9 2394718
9 2529275
9 2472219
10 2435365
10 2535348
9 2375662
10 2506714
11 2381437
11 2377332
11 2454308
11 2560280
8 2416217
10 2488674
11 2450364
10 2296417
11 2308479
18 2328405
17 2293804
16 2274121
19 2349084
18 2362136
15 2308122
13 2420087
13 2368169
10 2238414
11 2391400
11 2416125
11 2333381
11 2140508
12 2146874
11 2228809
12 2121568
13 1908897
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
14 2492008
13 2382753
13 2497154
15 2490485
13 2559055
12 2455844
12 2600300
12 2465145
14 2470709
13 2448554
14 2505407
13 2515047
12 2504338
12 2419091
12 2491698
12 2507461
11 2310513
11 2354595
12 2512715
11 2391203
11 2367371
10 2449527
10 2428928
8 2433405
10 2284607
11 2488577
11 2334725
11 2410332
10 2432416
11 2300942
11 2386533
11 2240271
11 2223724
11 2295242
11 2371810
12 2213713
12 2145391
10 1993757
11 2116591
10 1826063
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
17 3754574
18 3750606
17 3916745
14 3730691
16 3732333
18 3770747
15 3771464
16 3806221
13 3706860
13 3811369
13 3815660
14 3841974
13 3677613
13 3838177
12 3756178
12 3881102
10 4028934
10 3731276
10 3926973
10 3615494
10 3689952
11 3931163
9 3852721
9 3614753
9 3847291
10 3566262
11 3687182
10 3612176
10 3619302
11 3851497
10 3625908
10 3449372
11 3743028
9 3470305
9 3683821
9 3780161
9 3508395
8 3300690
8 3243804
7 2836780
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 5
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 1
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
12 12582912
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 10755918
FINISHED RECURSIVE SORTS: 1
RE-SORTED NODES: 8
PROCESS EDGES: 2
REMOVE Y: 1
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
12 12583320
12 12583501
12 12584237
12 12583556
12 12584805
12 12591380
12 12589096
12 12600459
12 12587365
12 12584340
12 12584140
12 12584115
12 12585251
12 12591919
12 12587333
12 12591274
12 12591646
12 12588680
12 12596117
12 12588701
12 12586174
12 12586478
12 12585851
12 12587500
11 11539030
11 11536572
11 11536889
11 11534736
11 11536211
11 11534794
11 11535454
11 11535065
11 11535036
11 11535177
11 11535068
11 11535101
11 11535181
11 11535679
11 11535218
11 10756587
FINISHED RECURSIVE SORTS: 1
SORT, Make index: 7
TOTAL: 31
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 147875828
fchr[G]: 243001481
fchr[T]: 338119481
fchr[$]: 485899035
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 303416084 bytes to primary GFM file: ../data/Phel_genome_index.1.ht2
Wrote 121440216 bytes to secondary GFM file: ../data/Phel_genome_index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Warning: a local graph exploded (offset: 121194950, length: 57344)
Warning: a local graph exploded (offset: 327235680, length: 57344)
Returning from initFromVector
Wrote 336934463 bytes to primary GFM file: ../data/Phel_genome_index.5.ht2
Wrote 123284342 bytes to secondary GFM file: ../data/Phel_genome_index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 483816647
    gbwtLen: 485899036
    nodes: 485760845
    sz: 241908324
    gbwtSz: 242949519
    lineRate: 7
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 30360053
    offsSz: 121440212
    lineSz: 128
    sideSz: 128
    sideGbwtSz: 104
    sideGbwtLen: 208
    numSides: 2336054
    numLines: 2336054
    gbwtTotLen: 299014912
    gbwtTotSz: 299014912
    reverse: 0
    linearFM: No
Total time for call to driver() for forward index: 00:07:15