Settings:
  Output files: "../output/01.5-lncRNA/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/01.5-lncRNA/genome.fasta
Reading reference sizes
  Time reading reference sizes: 00:00:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:01
  Time to read SNPs and splice sites: 00:00:01
Generation 0 (376743094 -> 376743094 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 1 (376906272 -> 376906272 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 2 (377232638 -> 377232638 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 3 (377885652 -> 377885652 nodes, 0 ranks)
BUILT FROM_INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 1
RESIZE NODES: 7
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
1 16480325
2 15540590
1 10832317
6 11628773
2 9368794
6 11772948
2 10804545
6 13510214
2 17456072
37 8605401
2 9941984
6 11457454
3 9114572
8 10457386
6 9180733
2 13407306
37 8494430
2 8697179
6 10580945
3 9426625
6 7227238
7 11766792
2 8521207
1 7439615
37 9261921
2 9424175
1 7627115
5 7971358
2 7844988
1 7302015
5 7944966
2 9545517
1 7655401
5 9274166
1 8506986
1 8603410
1 16518930
0 0
2 1
16 1
46 1
82 1
FINISHED RECURSIVE SORTS: 2
SORT NODES: 3
MERGE, UPDATE RANK: 6
Generation 4 (379194397 -> 378534816 nodes, 240705876 ranks)
ALLOCATE FROM_TABLE: 9
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 1
9 9507234
9 9480815
9 9507090
9 9482235
9 9505108
9 9497591
9 9499735
9 9494957
9 9469994
9 9473182
9 9483181
9 9496202
9 9494940
9 9495380
9 9481275
9 9492824
9 9453123
9 9468988
9 9499736
9 9500275
9 9467227
9 9478270
9 9496816
8 8437435
9 9482416
8 8434843
8 8436628
8 8429805
8 8432384
8 8428175
8 8420244
8 8417000
8 8444952
8 8428853
8 8442928
8 8438372
8 8436497
8 8438107
8 8432179
8 8431926
8 8401275
8 7494619
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: 2
MERGEUPDATERANK: 4
TOTAL TIME: 19
Generation 5 (378979682 -> 378592021 nodes, 307454446 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
9 9506975
9 9483068
9 9508566
9 9482343
9 9505577
9 9499181
9 9501760
9 9495104
9 9474084
9 9474016
9 9484150
9 9497110
9 9495277
9 9496696
9 9482347
9 9493864
9 9455711
9 9471462
9 9501001
9 9501117
9 9469007
9 9479548
9 9497039
9 9490796
8 8430752
8 8435951
8 8436963
8 8430452
8 8434040
8 8430263
8 8423012
8 8419480
8 8445579
8 8430325
8 8443719
8 8439757
8 8436882
8 8439521
8 8434558
8 8432182
8 8403296
8 7499490
FINISHED RECURSIVE SORTS: 0
BUILD TABLE: 2
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: 7
Generation 6 (378799003 -> 378727505 nodes, 334740479 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
9 9509805
9 9487858
9 9512056
9 9484184
9 9508532
9 9502773
9 9506177
9 9497328
9 9479025
9 9476114
9 9486975
9 9501361
9 9498163
9 9499906
9 9484689
9 9496976
9 9459219
9 9475030
9 9504172
9 9504117
9 9472207
9 9482884
9 9499675
9 9493771
8 8433216
8 8438731
8 8439626
8 8432513
8 8436809
8 8434117
8 8427077
8 8423098
8 8448920
8 8433529
8 8446887
8 8443446
8 8439037
8 8442560
8 8438608
8 8434153
8 8406151
8 7506030
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 7 (378918238 -> 378844707 nodes, 353899401 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
9 9512611
9 9492902
9 9515096
9 9485082
9 9510543
9 9505926
9 9509435
9 9498809
9 9484053
9 9477661
9 9489173
9 9505822
9 9501176
9 9502071
9 9486566
9 9499478
9 9461854
9 9477790
9 9506799
9 9506188
9 9474807
9 9486315
9 9502093
9 9496063
8 8435103
8 8441389
8 8441896
8 8434186
8 8438632
8 8436852
8 8430759
8 8426768
8 8451816
8 8436637
8 8449604
8 8446714
8 8441028
8 8445534
8 8441615
8 8435875
8 8409591
8 7512395
FINISHED RECURSIVE SORTS: 0
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 6
Generation 8 (379004130 -> 378942311 nodes, 364949704 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
9 9514923
9 9497401
9 9517182
9 9486033
9 9511820
9 9508780
9 9511341
9 9500502
9 9487400
9 9478662
9 9490650
9 9508661
9 9502932
9 9503637
9 9488920
9 9501171
9 9463418
9 9479588
9 9508318
9 9507576
9 9477613
9 9490569
9 9504386
9 9498142
8 8436711
8 8443074
8 8443987
8 8436455
8 8439894
8 8438795
8 8434280
8 8429677
8 8454074
8 8438886
8 8452246
8 8449922
8 8442312
8 8448953
8 8443610
8 8438232
8 8413938
8 7517640
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 9 (379070273 -> 379023413 nodes, 370753253 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 1
9 9516119
9 9500634
9 9518651
9 9487161
9 9512968
9 9511233
9 9512265
9 9502478
9 9489881
9 9479480
9 9491050
9 9509466
9 9504098
9 9505044
9 9491924
9 9502169
9 9464070
9 9480512
9 9508600
9 9509687
9 9480441
9 9495547
9 9504841
9 9499576
8 8437860
8 8443572
8 8445286
8 8438508
8 8441166
8 8440080
8 8436781
8 8432156
8 8454416
8 8441120
8 8454985
8 8451800
8 8442954
8 8452811
8 8446485
8 8441669
8 8420034
8 7523835
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 10 (379138588 -> 379094553 nodes, 374045257 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
9 9516791
9 9502236
9 9520024
9 9487947
9 9514251
9 9511492
9 9513310
9 9502726
9 9491391
9 9480395
9 9491820
9 9510211
9 9506157
9 9505367
9 9494243
9 9503231
9 9463487
9 9481169
9 9508526
9 9510911
9 9482358
9 9499701
9 9504143
9 9501345
8 8438671
8 8444633
8 8446514
8 8439429
8 8441769
8 8440417
8 8439011
8 8434186
8 8453876
8 8442478
8 8457542
8 8453980
8 8444977
8 8456643
8 8450012
8 8446447
8 8429023
8 7531713
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 8
Generation 11 (379197024 -> 379150175 nodes, 376054726 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
9 9515056
9 9503998
9 9519132
9 9487931
9 9517323
9 9510522
9 9514033
9 9502286
9 9492492
9 9480814
9 9491997
9 9510640
9 9506748
9 9505352
9 9495121
9 9504425
9 9464451
9 9482274
9 9508511
9 9511399
9 9484394
9 9500029
9 9504143
9 9500798
8 8438654
8 8445212
8 8445972
8 8440280
8 8443225
8 8441402
8 8441765
8 8435960
8 8453876
8 8444106
8 8459425
8 8455995
8 8447649
8 8459544
8 8453097
8 8450398
8 8439475
8 7540271
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 3
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 9
Generation 12 (379238581 -> 379187140 nodes, 377436170 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
9 9514711
9 9504390
9 9517655
9 9487931
9 9520036
9 9510522
9 9514033
9 9502286
9 9494540
9 9480814
9 9490850
9 9510640
9 9506137
9 9505352
9 9495417
9 9504425
9 9466499
9 9482590
9 9508511
9 9511619
9 9483937
9 9498448
9 9504143
9 9500789
8 8438654
8 8445212
8 8444769
8 8440431
8 8445273
8 8441175
8 8447909
8 8438142
8 8453876
8 8445984
8 8460846
8 8459389
8 8449860
8 8459860
8 8455415
8 8455192
8 8448530
8 7540348
FINISHED RECURSIVE SORTS: 0
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 3
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 2
TOTAL TIME: 9
Generation 13 (379279715 -> 379232727 nodes, 378492635 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
9 9514711
9 9503803
9 9517655
9 9487931
9 9521022
9 9510522
9 9514033
9 9502286
9 9494678
9 9480814
9 9490808
9 9510640
9 9506137
9 9505352
9 9491684
9 9504425
9 9470595
9 9482590
9 9508511
9 9511619
9 9481061
9 9498448
9 9504143
9 9500789
8 8438654
8 8445212
8 8444769
8 8440431
8 8448678
8 8441175
8 8458220
8 8438897
8 8453876
8 8447607
8 8464134
8 8467327
8 8449860
8 8462843
8 8452070
8 8461937
8 8458719
8 7544061
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 4
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 1
TOTAL TIME: 8
Generation 14 (379304138 -> 379248130 nodes, 379116739 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
9 9514711
9 9500283
9 9517655
9 9487931
9 9521022
9 9510522
9 9514033
9 9502286
9 9490456
9 9480814
9 9490808
9 9510640
9 9506137
9 9505352
9 9491068
9 9504425
9 9478787
9 9482590
9 9508511
9 9511619
9 9481061
9 9498448
9 9504143
9 9500789
8 8438654
8 8445212
8 8444769
8 8440431
8 8448678
8 8441175
8 8466237
8 8438777
8 8453876
8 8447607
8 8472326
8 8467327
8 8449860
8 8459329
8 8452070
8 8454600
8 8475926
8 7537185
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 15 (379273989 -> 379258951 nodes, 379258951 ranks)
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 2
9 9514711
9 9500283
9 9517655
9 9487931
9 9521022
9 9510522
9 9514033
9 9502286
9 9490456
9 9480814
9 9490808
9 9510640
9 9506137
9 9505352
9 9491068
9 9504425
9 9479517
9 9482590
9 9508511
9 9511619
9 9481061
9 9498448
9 9504143
9 9500789
8 8438654
8 8445212
8 8444769
8 8440431
8 8448678
8 8441175
8 8473741
8 8434059
8 8453876
8 8447607
8 8479830
8 8467327
8 8449860
8 8459329
8 8449585
8 8454600
8 8481037
8 7534360
FINISHED RECURSIVE SORTS: 1
Generating edges... 
NODE.TO -> GENOME POS: 2
BUILD FROM_INDEX 1
COUNTED NEW EDGES: 0
MADE NEW EDGES: 3
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
7 2824571
8 3113831
7 2828527
8 3145313
7 2974264
7 2850260
8 2899841
8 2967274
8 3089831
8 2967271
8 3032629
8 2981673
8 2806899
8 2981910
8 2784307
9 2843012
9 2831999
9 2741710
9 2728785
9 2714193
10 2927770
10 2927726
8 2722644
8 2673447
9 2900060
9 2984446
8 2725558
8 2650842
9 2807173
9 2870040
9 2768365
10 2856456
8 2560752
10 2746832
10 2585291
9 2532688
10 2747481
10 2661064
10 2581622
10 2521120
9 2485887
8 2121337
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
9 1849525
9 1919085
8 1744334
8 1725536
9 1809121
8 1824772
8 1906934
8 1832424
7 1755938
7 1792400
8 1714097
8 1883187
8 1830838
8 1774484
9 1792959
9 1837853
9 1782343
8 1737803
9 1699237
9 1827624
9 1843190
9 1686283
11 1673743
11 1714798
10 1692352
12 1672959
11 1674761
11 1666439
10 1759599
9 1619487
10 1766229
8 1721055
7 1643782
8 1770804
7 1587856
8 1756195
8 1644053
8 1531565
7 1486988
7 1431525
8 1590173
7 1229152
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
8 1776482
8 1769716
9 1780468
9 1864949
9 1733111
9 1738806
9 1765685
8 1856088
8 1817864
9 1851694
9 1826830
8 1699091
10 1819849
9 1784868
9 1778962
9 1807275
9 1797148
8 1788036
8 1723053
8 1696192
9 1812653
8 1710312
9 1808185
9 1744196
8 1639931
9 1891610
8 1639966
8 1631018
9 1705549
8 1717084
9 1818596
9 1657927
9 1654295
9 1574079
9 1693146
8 1546380
9 1697851
9 1703473
9 1489507
8 1513194
9 1631172
7 1236159
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
13 2893648
13 2949740
13 2936981
11 2804325
12 2929299
14 2837662
13 2940344
11 2785943
11 2960527
9 2850823
9 3007797
9 3057580
9 3019574
9 3039109
9 3048676
9 3000565
8 2806444
8 2847638
8 2787409
7 2700627
8 2760853
8 2829717
8 2931307
7 2701105
8 2950193
7 2755669
8 2835471
7 2659737
8 2993523
8 2989018
7 2734866
7 2735526
8 2820990
8 2841270
7 2578172
7 2788985
6 2445561
6 2613377
6 2369104
6 2388999
6 2331975
6 2300651
FINISHED RECURSIVE SORTS: 1
SORTED NEW EDGES: 4
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 1
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8063047
FINISHED RECURSIVE SORTS: 1
RE-SORTED NODES: 5
PROCESS EDGES: 2
REMOVE Y: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
9 9437611
9 9437851
9 9438435
9 9438531
9 9438081
9 9447579
9 9440919
9 9450532
9 9457189
9 9439506
9 9438391
9 9438251
9 9438746
9 9441932
9 9445398
9 9444184
9 9452895
9 9440273
9 9448310
9 9451976
9 9440778
9 9440153
9 9440710
9 9439983
9 9443394
9 9442877
8 8391069
8 8391139
8 8388896
8 8390615
8 8389148
8 8389836
8 8389110
8 8389197
8 8389196
8 8389251
8 8389195
8 8389452
8 8389586
8 8390005
8 8389393
8 8063841
FINISHED RECURSIVE SORTS: 1
SORT, Make index: 5
TOTAL: 22
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 117466701
fchr[G]: 189670183
fchr[T]: 261862633
fchr[$]: 379423413
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 237697865 bytes to primary GFM file: ../output/01.5-lncRNA/genome.index.1.ht2
Wrote 94814744 bytes to secondary GFM file: ../output/01.5-lncRNA/genome.index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Warning: a local graph exploded (offset: 322184488, length: 57344)
Returning from initFromVector
Wrote 256383163 bytes to primary GFM file: ../output/01.5-lncRNA/genome.index.5.ht2
Wrote 96078770 bytes to secondary GFM file: ../output/01.5-lncRNA/genome.index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 376579914
    gbwtLen: 379423414
    nodes: 379258950
    sz: 188289957
    gbwtSz: 189711708
    lineRate: 7
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 23703685
    offsSz: 94814740
    lineSz: 128
    sideSz: 128
    sideGbwtSz: 104
    sideGbwtLen: 208
    numSides: 1824152
    numLines: 1824152
    gbwtTotLen: 233491456
    gbwtTotSz: 233491456
    reverse: 0
    linearFM: No
Total time for call to driver() for forward index: 00:05:41