Settings:
  Output files: "../output/24-Apul-lncRNA-rediscovery/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/24-Apul-lncRNA-rediscovery/genome.fasta
Reading reference sizes
  Time reading reference sizes: 00:00:07
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:05
  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: 7
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 1 (475704030 -> 475704030 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 6
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 2 (476062897 -> 476062897 nodes, 0 ranks)
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 6
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 3 (476780929 -> 476780929 nodes, 0 ranks)
BUILT FROM_INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 8
RESIZED NODES: 0
MADE NEW NODES: 1
RESIZE NODES: 16
COUNT NUMBER IN EACH BIN: 1
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
2 8747433
6 11213737
2 15342674
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
0 0
0 0
46 1
100 1
FINISHED RECURSIVE SORTS: 5
SORT NODES: 7
MERGE, UPDATE RANK: 14
Generation 4 (478218330 -> 477533289 nodes, 274482571 ranks)
ALLOCATE FROM_TABLE: 13
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 2
11 11607647
11 11601737
11 11571624
11 11618954
11 11581956
11 11610196
11 11620359
11 11581737
11 11611936
11 11591615
11 11605795
11 11596845
11 11577486
11 11610241
11 11603005
11 11597922
11 11579686
11 11593507
11 11618054
11 11601335
11 11590696
11 11563615
11 11585253
11 11589124
11 11596274
11 11618149
11 11603009
11 11602481
11 11600581
11 11586821
11 11557162
11 11557591
11 11560840
11 11558693
10 10506432
10 10505933
10 10537768
10 10509674
10 10511616
10 10504651
10 10512553
10 9792736
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 2
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 3
MERGEUPDATERANK: 12
TOTAL TIME: 35
Generation 5 (478110321 -> 477627123 nodes, 369324915 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
11 11608823
11 11602322
11 11573820
11 11617859
11 11584377
11 11609112
11 11619926
11 11582470
11 11612155
11 11594014
11 11607136
11 11600188
11 11580082
11 11611530
11 11602843
11 11600827
11 11581130
11 11595918
11 11617886
11 11604284
11 11593821
11 11566766
11 11588590
11 11590878
11 11597398
11 11617942
11 11605210
11 11602799
11 11601765
11 11590564
11 11561479
11 11562097
11 11565221
11 11562673
10 10510871
10 10510140
10 10540795
10 10514340
10 10516515
10 10508782
10 10515366
10 9796409
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 5
BUILD INDEX: 2
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 8
TOTAL TIME: 18
Generation 6 (477918190 -> 477811099 nodes, 415777011 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
11 11612688
11 11605854
11 11577804
11 11621043
11 11588687
11 11611172
11 11623121
11 11584905
11 11615408
11 11598339
11 11611392
11 11605475
11 11584580
11 11615564
11 11605702
11 11606064
11 11584249
11 11600532
11 11621613
11 11609343
11 11598649
11 11571234
11 11593303
11 11594878
11 11601075
11 11621204
11 11610365
11 11606344
11 11605954
11 11596336
11 11567065
11 11567749
11 11570604
11 11567545
10 10516335
10 10516196
10 10546248
10 10520350
10 10522402
10 10514091
10 10519096
10 9800541
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 5
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: 15
Generation 7 (478079456 -> 477971301 nodes, 446951947 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 3
11 11616145
11 11609391
11 11581216
11 11623937
11 11592276
11 11612884
11 11626230
11 11586600
11 11617779
11 11601877
11 11613683
11 11610774
11 11588342
11 11617947
11 11608262
11 11610790
11 11587204
11 11605034
11 11624679
11 11614035
11 11602706
11 11575573
11 11596398
11 11597571
11 11603839
11 11623240
11 11614320
11 11609759
11 11610244
11 11601612
11 11572797
11 11572650
11 11574908
11 11571702
10 10520434
10 10522559
10 10551541
10 10525741
10 10528318
10 10519771
10 10522608
10 9803925
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 6
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 3
TOTAL TIME: 13
Generation 8 (478173458 -> 478077067 nodes, 464194559 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
11 11618525
11 11612440
11 11582944
11 11626003
11 11594956
11 11613768
11 11628524
11 11587252
11 11619131
11 11603504
11 11614729
11 11614242
11 11590062
11 11618833
11 11609889
11 11613714
11 11589390
11 11608504
11 11626973
11 11617777
11 11604212
11 11578475
11 11597758
11 11599337
11 11606513
11 11624844
11 11617265
11 11612008
11 11612791
11 11604873
11 11577528
11 11576824
11 11577866
11 11573246
10 10522207
10 10526330
10 10555482
10 10529923
10 10533351
10 10523900
10 10525204
10 9805970
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 5
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 3
TOTAL TIME: 12
Generation 9 (478209494 -> 478136978 nodes, 472225209 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
11 11619324
11 11614279
11 11584522
11 11628603
11 11595951
11 11614252
11 11629595
11 11587909
11 11620557
11 11603685
11 11614842
11 11615664
11 11590252
11 11619230
11 11610466
11 11615256
11 11590828
11 11612119
11 11628141
11 11619877
11 11603941
11 11579341
11 11598893
11 11599969
11 11608711
11 11627034
11 11618344
11 11614297
11 11614245
11 11605695
11 11580032
11 11578920
11 11579845
11 11574259
10 10523919
10 10529230
10 10557016
10 10531799
10 10536729
10 10526244
10 10527136
10 9806027
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 4
BUILD INDEX: 2
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 7
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 4
TOTAL TIME: 19
Generation 10 (478218533 -> 478168919 nodes, 475784458 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
11 11619391
11 11614665
11 11586494
11 11629951
11 11595882
11 11614781
11 11630191
11 11588421
11 11621338
11 11604322
11 11614842
11 11614855
11 11590124
11 11620254
11 11609713
11 11616736
11 11590516
11 11615519
11 11628758
11 11622022
11 11603908
11 11581414
11 11600530
11 11600597
11 11610914
11 11628212
11 11618477
11 11615767
11 11614400
11 11605320
11 11580695
11 11579392
11 11581947
11 11574583
10 10525938
10 10529720
10 10556734
10 10532544
10 10539055
10 10526393
10 10528488
10 9805116
FINISHED RECURSIVE SORTS: 2
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: 2
TOTAL TIME: 11
Generation 11 (478210121 -> 478178514 nodes, 477322472 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 3
11 11620379
11 11615002
11 11585935
11 11631116
11 11595878
11 11615437
11 11630191
11 11588243
11 11621338
11 11605053
11 11614842
11 11614843
11 11589994
11 11622218
11 11609196
11 11617611
11 11590093
11 11615868
11 11628758
11 11623812
11 11604205
11 11580654
11 11600948
11 11600558
11 11611567
11 11627669
11 11618477
11 11616964
11 11614340
11 11605984
11 11581581
11 11579681
11 11582565
11 11574583
10 10525070
10 10528428
10 10557710
10 10532084
10 10539292
10 10525730
10 10529590
10 9805027
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 6
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 4
TOTAL TIME: 14
Generation 12 (478188202 -> 478169611 nodes, 477903667 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
11 11620669
11 11615002
11 11585446
11 11631236
11 11595878
11 11615437
11 11630191
11 11587410
11 11621338
11 11605053
11 11614842
11 11614843
11 11589455
11 11622595
11 11609196
11 11615588
11 11589823
11 11614532
11 11628758
11 11624449
11 11604205
11 11580271
11 11600790
11 11600558
11 11611268
11 11627027
11 11618477
11 11617761
11 11614340
11 11605984
11 11580458
11 11579655
11 11581063
11 11574583
10 10525070
10 10527757
10 10557710
10 10530624
10 10539572
10 10525500
10 10530170
10 9805027
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 5
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 3
MERGEUPDATERANK: 4
TOTAL TIME: 14
Generation 13 (478169634 -> 478167510 nodes, 478101240 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
11 11620669
11 11615002
11 11585446
11 11631236
11 11595878
11 11615437
11 11630191
11 11587410
11 11621338
11 11605053
11 11614842
11 11614625
11 11589455
11 11622595
11 11609196
11 11615588
11 11589823
11 11614532
11 11628758
11 11624449
11 11604205
11 11580271
11 11600790
11 11600558
11 11611268
11 11627027
11 11618477
11 11617761
11 11614340
11 11605984
11 11580458
11 11579655
11 11581063
11 11574583
10 10525070
10 10527757
10 10557710
10 10530137
10 10538176
10 10525500
10 10530170
10 9805027
FINISHED RECURSIVE SORTS: 2
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: 4
TOTAL TIME: 13
Generation 14 (478167510 -> 478167510 nodes, 478166970 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 3
11 11620669
11 11615002
11 11585446
11 11631236
11 11595878
11 11615437
11 11630191
11 11587410
11 11621338
11 11605053
11 11614842
11 11614625
11 11589455
11 11622595
11 11609196
11 11615588
11 11589823
11 11614532
11 11628758
11 11624449
11 11604205
11 11580271
11 11600790
11 11600558
11 11611268
11 11627027
11 11618477
11 11617761
11 11614340
11 11605984
11 11580458
11 11579655
11 11581063
11 11574583
10 10525070
10 10527757
10 10557710
10 10530137
10 10538176
10 10525500
10 10530170
10 9805027
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 5
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 3
MERGEUPDATERANK: 3
TOTAL TIME: 13
Generation 15 (478167510 -> 478167510 nodes, 478167510 ranks)
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 2
11 11620669
11 11615002
11 11585446
11 11631236
11 11595878
11 11615437
11 11630191
11 11587410
11 11621338
11 11605053
11 11614842
11 11614625
11 11589455
11 11622595
11 11609196
11 11615588
11 11589823
11 11614532
11 11628758
11 11624449
11 11604205
11 11580271
11 11600790
11 11600558
11 11611268
11 11627027
11 11618477
11 11617761
11 11614340
11 11605984
11 11580458
11 11579655
11 11581063
11 11574583
10 10525070
10 10527757
10 10557710
10 10530137
10 10538176
10 10525500
10 10530170
10 9805027
FINISHED RECURSIVE SORTS: 2
Generating edges... 
NODE.TO -> GENOME POS: 3
BUILD FROM_INDEX 1
COUNTED NEW EDGES: 1
MADE NEW EDGES: 8
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
9 3571529
9 3527092
9 3627931
9 3475124
9 3726433
9 3674672
10 3613674
10 3642485
9 3461463
10 3702453
10 3709896
9 3588793
10 3546598
10 3735951
10 3401611
11 3476001
12 3624431
12 3623211
12 3443524
12 3578091
12 3435460
12 3578078
11 3442722
11 3474509
11 3419810
11 3419918
11 3574240
11 3432806
12 3591539
11 3429842
11 3394280
12 3541415
11 3486451
12 3212224
13 3258214
12 3349173
12 3215887
12 3214345
12 3282981
13 3176561
12 3255109
11 2793179
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
11 2436768
10 2268916
10 2356554
10 2273140
11 2364022
10 2299151
9 2211104
10 2370132
9 2277066
9 2249508
10 2288014
10 2351198
10 2312071
10 2428674
12 2389976
11 2372899
11 2275272
11 2338178
11 2162234
12 2341635
10 2154451
11 2337697
14 2236358
13 2278814
13 2225877
14 2216744
14 2182976
12 2098792
13 2163463
12 2193560
12 2145200
12 2247224
10 2295245
10 2209869
10 2112091
10 2168523
10 2140328
11 2059181
9 1940279
10 2040237
10 1958770
10 1660243
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 2266065
11 2401847
11 2271792
12 2400916
12 2328675
11 2340935
11 2251638
10 2254970
10 2240443
12 2350826
11 2261849
12 2246826
11 2220317
11 2360041
11 2361616
10 2263390
10 2222202
10 2316020
10 2315478
10 2242542
10 2177796
11 2377822
11 2284156
11 2172355
10 2150218
11 2312719
11 2289208
11 2254612
11 2234551
11 2217068
11 2247001
11 2096075
11 2188764
12 2230720
11 2096904
11 2122473
11 2169782
11 2057863
12 2057861
11 2107704
11 2017165
10 1719044
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
17 3490144
17 3563748
16 3644491
15 3621283
16 3510277
17 3506725
15 3602518
15 3590122
13 3662922
12 3716391
11 3482338
11 3573829
11 3545632
11 3580109
11 3567530
11 3514964
10 3409930
10 3561704
10 3450981
9 3410503
10 3482533
10 3551862
10 3664199
9 3441030
10 3623259
9 3492033
10 3532909
10 3646086
10 3644847
9 3436569
9 3505915
9 3418232
9 3306859
9 3354296
9 3214167
9 3510309
9 3549800
8 3469730
8 3154627
8 3171640
8 3109492
7 2399020
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 8
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 1
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 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
10 10485760
10 10485760
10 10485760
10 10485760
10 9454038
FINISHED RECURSIVE SORTS: 2
RE-SORTED NODES: 11
PROCESS EDGES: 4
REMOVE Y: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
11 11534893
11 11535193
11 11535737
11 11535970
11 11535247
11 11545920
11 11537531
11 11547836
11 11556105
11 11538256
11 11535701
11 11535523
11 11535929
11 11537258
11 11544445
11 11540631
11 11551640
11 11538002
11 11539853
11 11548715
11 11547637
11 11537211
11 11538085
11 11537324
11 11537269
11 11540445
11 11540221
11 11537186
11 11536959
11 11535167
11 11536329
11 11535010
11 11535680
11 11535124
11 11535019
11 11535208
11 11535131
10 10486766
10 10486901
10 10487184
10 10486768
10 9454936
FINISHED RECURSIVE SORTS: 2
SORT, Make index: 10
TOTAL: 47
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: ../output/24-Apul-lncRNA-rediscovery/genome.index.1.ht2
Wrote 119541884 bytes to secondary GFM file: ../output/24-Apul-lncRNA-rediscovery/genome.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: ../output/24-Apul-lncRNA-rediscovery/genome.index.5.ht2
Wrote 121199738 bytes to secondary GFM file: ../output/24-Apul-lncRNA-rediscovery/genome.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: 00:14:54