Settings:
  Output files: "../data/GCF_013753865.1_Amil_v2.1.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/GCF_013753865.1_Amil_v2.1_genomic.fna
Reading reference sizes
  Time reading reference sizes: 00:00:06
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:03
  Time to read SNPs and splice sites: 00:00:02
Generation 0 (475524637 -> 475524637 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 4
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 1 (475704030 -> 475704030 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 2 (476062897 -> 476062897 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 3 (476780929 -> 476780929 nodes, 0 ranks)
BUILT FROM_INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 4
RESIZED NODES: 0
MADE NEW NODES: 0
RESIZE NODES: 8
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
1 20188405
2 19286429
1 13508540
6 14661999
2 11922180
6 14586116
2 13271917
6 16355593
2 21911668
37 11385970
2 12675031
6 14869491
3 11916438
7 10496335
7 15484049
2 16582952
37 10553510
2 11082692
6 13726103
3 13146398
6 9665506
7 14769438
2 11226709
1 9307697
37 10843470
2 11429384
1 9308883
5 9752495
2 10250715
1 8640764
5 9770947
2 13159692
1 9552272
5 10836794
1 10539242
1 11380357
1 20172147
0 0
46 1
100 1
FINISHED RECURSIVE SORTS: 2
SORT NODES: 3
MERGE, UPDATE RANK: 8
Generation 4 (478218330 -> 477533289 nodes, 274482571 ranks)
ALLOCATE FROM_TABLE: 9
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 1
12 12665477
12 12647767
12 12634789
12 12662404
12 12652905
12 12655282
12 12669147
12 12652867
12 12645923
12 12660181
12 12653659
12 12633737
12 12661032
11 11609132
12 12639549
11 11591575
11 11582718
11 11634678
11 11584457
11 11585646
11 11572139
11 11582492
11 11603629
11 11586807
11 11623433
11 11595465
11 11621790
11 11580836
11 11578415
11 11560322
11 11555908
11 11560414
11 11560718
11 11553532
11 11570870
11 11579277
11 11561371
11 11556142
11 11563958
11 10842846
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 3
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 6
TOTAL TIME: 22
Generation 5 (478110321 -> 477627123 nodes, 369324915 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
12 12666499
12 12648726
12 12636489
12 12662718
12 12653441
12 12655267
12 12668440
12 12653735
12 12648215
12 12661781
12 12656891
12 12636490
12 12662003
11 11609038
12 12643003
11 11592550
11 11586332
11 11633347
11 11588778
11 11587913
11 11576131
11 11585050
11 11604180
11 11588926
11 11622737
11 11597918
11 11621195
11 11583273
11 11583090
11 11564266
11 11560664
11 11565023
11 11564733
11 11558410
11 11575707
11 11582172
11 11567346
11 11560312
11 11567431
11 10846903
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: 4
TOTAL TIME: 9
Generation 6 (477918190 -> 477811099 nodes, 415777011 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
12 12670644
12 12652594
12 12640689
12 12666778
12 12656539
12 12658672
12 12670924
12 12657483
12 12652618
12 12666334
12 12662613
12 12641375
12 12665965
11 11612264
12 12648493
11 11595407
11 11591947
11 11636565
11 11594129
11 11591900
11 11581329
11 11589728
11 11607382
11 11593043
11 11625802
11 11603007
11 11624613
11 11587743
11 11589990
11 11569575
11 11566239
11 11570593
11 11569807
11 11564796
11 11582367
11 11587629
11 11574202
11 11565801
11 11572091
11 10851429
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 3
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 3
TOTAL TIME: 8
Generation 7 (478079456 -> 477971301 nodes, 446951947 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
12 12674413
12 12656293
12 12644364
12 12670156
12 12659074
12 12662163
12 12672918
12 12660356
12 12656126
12 12668776
12 12668153
12 12645240
12 12668612
11 11614909
12 12653949
11 11597699
11 11597453
11 11639178
11 11598984
11 11595322
11 11585805
11 11593128
11 11609225
11 11596014
11 11627772
11 11607259
11 11627671
11 11592552
11 11596878
11 11574813
11 11570315
11 11575686
11 11573875
11 11570269
11 11588608
11 11593185
11 11580753
11 11571259
11 11577050
11 10855046
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: 2
TOTAL TIME: 7
Generation 8 (478173458 -> 478077067 nodes, 464194559 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
12 12677149
12 12659530
12 12645882
12 12672842
12 12660937
12 12664196
12 12674272
12 12661563
12 12658029
12 12670111
12 12671507
12 12647056
12 12669478
11 11616819
12 12656947
11 11599938
11 11601506
11 11640922
11 11603001
11 11596467
11 11588417
11 11594816
11 11610664
11 11599051
11 11628840
11 11610857
11 11629422
11 11595523
11 11601650
11 11579581
11 11572808
11 11578763
11 11576207
11 11572726
11 11591434
11 11598961
11 11585657
11 11575357
11 11580993
11 10857188
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 3
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 2
TOTAL TIME: 7
Generation 9 (478209494 -> 478136978 nodes, 472225209 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
12 12677960
12 12661855
12 12647882
12 12674705
12 12662000
12 12665274
12 12674679
12 12662762
12 12658805
12 12670525
12 12672736
12 12647194
12 12669799
11 11617879
12 12658146
11 11601646
11 11604697
11 11642246
11 11604830
11 11596275
11 11589918
11 11595006
11 11611642
11 11601791
11 11630492
11 11612904
11 11630930
11 11596736
11 11603731
11 11582133
11 11574057
11 11581301
11 11577077
11 11574482
11 11593336
11 11601814
11 11588633
11 11578530
11 11583094
11 10857476
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 3
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 4
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 2
TOTAL TIME: 10
Generation 10 (478218533 -> 478168919 nodes, 475784458 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
12 12678027
12 12662514
12 12650230
12 12675325
12 12662108
12 12666460
12 12674520
12 12663338
12 12660160
12 12670524
12 12671927
12 12647066
12 12670823
11 11617250
12 12659197
11 11601774
11 11608367
11 11641949
11 11607240
11 11596461
11 11592223
11 11596381
11 11612325
11 11604189
11 11631324
11 11614525
11 11631045
11 11596677
11 11603415
11 11582564
11 11575446
11 11583553
11 11577704
11 11574976
11 11594254
11 11602602
11 11590074
11 11578863
11 11584954
11 10856565
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 3
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 6
Generation 11 (478210121 -> 478178514 nodes, 477322472 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 1
12 12679015
12 12662631
12 12649808
12 12676573
12 12662104
12 12667116
12 12674520
12 12663160
12 12660891
12 12670524
12 12671915
12 12646936
12 12672787
11 11616733
12 12660072
11 11601296
11 11608771
11 11641949
11 11609030
11 11596758
11 11590645
11 11597617
11 11612286
11 11604222
11 11631401
11 11616312
11 11630455
11 11596617
11 11604189
11 11583340
11 11576759
11 11583147
11 11577258
11 11574284
11 11593915
11 11602724
11 11589587
11 11578593
11 11586098
11 10856476
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 3
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 7
Generation 12 (478188202 -> 478169611 nodes, 477903667 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
12 12679305
12 12662563
12 12649387
12 12676693
12 12662104
12 12667116
12 12674520
12 12662327
12 12660891
12 12670524
12 12671915
12 12646397
12 12673164
11 11616564
12 12658218
11 11601026
11 11607435
11 11641949
11 11609667
11 11596758
11 11590104
11 11597617
11 11612286
11 11603844
11 11630838
11 11617163
11 11630401
11 11596617
11 11603066
11 11583340
11 11577035
11 11581343
11 11577258
11 11574284
11 11593244
11 11601264
11 11589867
11 11578363
11 11586678
11 10856476
FINISHED RECURSIVE SORTS: 1
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: 2
TOTAL TIME: 7
Generation 13 (478169634 -> 478167510 nodes, 478101240 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
12 12679305
12 12662563
12 12649387
12 12676693
12 12662104
12 12667116
12 12674520
12 12662327
12 12660891
12 12670524
12 12671697
12 12646397
12 12673164
11 11616564
12 12658218
11 11601026
11 11607435
11 11641949
11 11609667
11 11596758
11 11590104
11 11597617
11 11612286
11 11603844
11 11630838
11 11617163
11 11630401
11 11596617
11 11603066
11 11583340
11 11577035
11 11581343
11 11577258
11 11574284
11 11593244
11 11600777
11 11589140
11 11577694
11 11586678
11 10856476
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 3
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 6
Generation 14 (478167510 -> 478167510 nodes, 478166970 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 1
12 12679305
12 12662563
12 12649387
12 12676693
12 12662104
12 12667116
12 12674520
12 12662327
12 12660891
12 12670524
12 12671697
12 12646397
12 12673164
11 11616564
12 12658218
11 11601026
11 11607435
11 11641949
11 11609667
11 11596758
11 11590104
11 11597617
11 11612286
11 11603844
11 11630838
11 11617163
11 11630401
11 11596617
11 11603066
11 11583340
11 11577035
11 11581343
11 11577258
11 11574284
11 11593244
11 11600777
11 11589140
11 11577694
11 11586678
11 10856476
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: 1
MERGEUPDATERANK: 1
TOTAL TIME: 7
Generation 15 (478167510 -> 478167510 nodes, 478167510 ranks)
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
12 12679305
12 12662563
12 12649387
12 12676693
12 12662104
12 12667116
12 12674520
12 12662327
12 12660891
12 12670524
12 12671697
12 12646397
12 12673164
11 11616564
12 12658218
11 11601026
11 11607435
11 11641949
11 11609667
11 11596758
11 11590104
11 11597617
11 11612286
11 11603844
11 11630838
11 11617163
11 11630401
11 11596617
11 11603066
11 11583340
11 11577035
11 11581343
11 11577258
11 11574284
11 11593244
11 11600777
11 11589140
11 11577694
11 11586678
11 10856476
FINISHED RECURSIVE SORTS: 1
Generating edges... 
NODE.TO -> GENOME POS: 1
BUILD FROM_INDEX 2
COUNTED NEW EDGES: 0
MADE NEW EDGES: 4
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 3963480
10 3940769
10 3990151
10 3895714
9 3829143
10 3840201
11 3922598
10 3817188
10 3657122
10 3772159
9 3584423
11 3902398
10 3775257
11 3797520
12 3793583
12 3624431
12 3623211
13 3764785
12 3566898
13 3766327
13 3761113
11 3559731
11 3477908
12 3712638
12 3763746
11 3550910
12 3730407
12 3614469
12 3675380
12 3619313
11 3507922
12 3385231
14 3512838
13 3536137
13 3501782
13 3484993
12 3282981
13 3176561
12 3255109
11 2793179
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
11 2436768
11 2514900
10 2349696
11 2496656
11 2333574
10 2369186
10 2459971
10 2341613
10 2505666
9 2363939
11 2335078
10 2432903
10 2333778
11 2371596
11 2337785
11 2352810
12 2458632
12 2447453
12 2342379
11 2335740
11 2290908
14 2350443
13 2308247
14 2306354
14 2304357
15 2358339
13 2259450
14 2341311
13 2393299
13 2291111
12 2397592
10 2325452
11 2337914
11 2382392
10 2189099
11 2164224
11 2215491
11 2286745
11 2138221
11 1871362
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
11 2496693
11 2358897
12 2541871
13 2489966
12 2395003
11 2348127
11 2344197
11 2462354
11 2320140
12 2329984
11 2315951
14 2523285
11 2444083
11 2371812
11 2358354
10 2299687
11 2500151
11 2516618
11 2501215
11 2390965
11 2382479
11 2265353
12 2372586
11 2396366
11 2247430
11 2329397
11 2258703
12 2349778
11 2290060
11 2297370
12 2209422
12 2302608
12 2219932
12 2364751
11 2199790
12 2229803
12 2120368
12 2208771
12 2243434
11 1902495
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
18 3697335
18 3767166
16 3703668
16 3794440
17 3680013
18 3757402
15 3827115
15 3700256
13 3789130
12 3763233
12 3906578
12 3792276
11 3621799
12 3890482
12 3848779
11 3706359
11 3898626
11 3835740
10 3767295
11 3772823
10 3657991
10 3674963
10 3796074
10 3634827
10 3787022
10 3582219
10 3483315
9 3509512
9 3447335
10 3789826
9 3477926
10 3611674
10 3601288
9 3481798
9 3479647
8 3432211
8 3265379
9 3552998
8 3140200
8 2758835
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 4
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
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 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 11534336
11 10502614
FINISHED RECURSIVE SORTS: 1
RE-SORTED NODES: 7
PROCESS EDGES: 2
REMOVE Y: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
12 12583582
12 12583941
12 12585099
12 12583759
12 12585309
12 12593567
12 12595655
12 12605782
12 12588656
12 12584348
12 12584214
12 12584716
12 12586517
12 12593154
12 12590435
12 12600274
12 12586360
11 11545196
11 11550795
11 11539617
11 11537341
11 11538200
11 11536774
11 11539715
11 11541707
11 11536679
11 11537601
11 11535447
11 11536387
11 11535134
11 11535784
11 11534966
11 11535129
11 11535177
11 11535170
11 11535375
11 11535449
11 11535800
11 11535487
11 10503647
FINISHED RECURSIVE SORTS: 1
SORT, Make index: 6
TOTAL: 27
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 145729706
fchr[G]: 239162140
fchr[T]: 332662389
fchr[$]: 478347944
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 298688714 bytes to primary GFM file: ../data/GCF_013753865.1_Amil_v2.1.index.1.ht2
Wrote 119541884 bytes to secondary GFM file: ../data/GCF_013753865.1_Amil_v2.1.index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 332322157 bytes to primary GFM file: ../data/GCF_013753865.1_Amil_v2.1.index.5.ht2
Wrote 121199738 bytes to secondary GFM file: ../data/GCF_013753865.1_Amil_v2.1.index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 475342477
    gbwtLen: 478347945
    nodes: 478167509
    sz: 237671239
    gbwtSz: 239173973
    lineRate: 7
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 29885470
    offsSz: 119541880
    lineSz: 128
    sideSz: 128
    sideGbwtSz: 104
    sideGbwtLen: 208
    numSides: 2299750
    numLines: 2299750
    gbwtTotLen: 294368000
    gbwtTotSz: 294368000
    reverse: 0
    linearFM: No
Total time for call to driver() for forward index: 00:08:19