Settings:
  Output files: "../output/17-Ptuh-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/17-Ptuh-lncRNA/genome.fasta
Reading reference sizes
  Time reading reference sizes: 00:00:02
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: 00:00:02
Generation 0 (376743094 -> 376743094 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 1 (376906272 -> 376906272 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 2 (377232638 -> 377232638 nodes, 0 ranks)
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 3 (377885652 -> 377885652 nodes, 0 ranks)
BUILT FROM_INDEX: 0
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
RESIZE NODES: 2
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
1 16480325
3 26372907
8 20997567
7 16280846
7 19806861
2 17456072
39 18547385
8 16067487
9 14961925
7 14507364
38 16575105
3 14590596
8 14114153
8 13965493
8 20989359
38 14300112
7 19984457
3 15147003
6 12636982
2 12508902
6 17781152
1 8603410
1 16518930
146 4
FINISHED RECURSIVE SORTS: 2
SORT NODES: 2
MERGE, UPDATE RANK: 4
Generation 4 (379194397 -> 378534816 nodes, 240705876 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15820604
15 15836120
15 15825758
15 15825422
15 15820521
15 15789516
15 15818026
15 15823204
15 15809748
15 15796782
15 15778237
15 15839927
15 15783766
15 15821924
15 15809530
15 15818415
15 15808563
15 15797806
15 15797033
15 15812131
15 15838087
15 15815402
15 15806323
15 14841971
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
BUILD INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 3
TOTAL TIME: 5
Generation 5 (378979682 -> 378592021 nodes, 307454446 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15822719
15 15837507
15 15826303
15 15829074
15 15822473
15 15792598
15 15819134
15 15824664
15 15811782
15 15799716
15 15781685
15 15841754
15 15786630
15 15822455
15 15811482
15 15819489
15 15810609
15 15801855
15 15801607
15 15814315
15 15839179
15 15817626
15 15808545
15 14848820
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
BUILD INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 3
Generation 6 (378799003 -> 378727505 nodes, 334740479 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
15 15829598
15 15842323
15 15830514
15 15836011
15 15827473
15 15797933
15 15824625
15 15829970
15 15816499
15 15805308
15 15787314
15 15846892
15 15792132
15 15826991
15 15816768
15 15824219
15 15815095
15 15808786
15 15808938
15 15820478
15 15844807
15 15822706
15 15814224
15 14857901
FINISHED RECURSIVE SORTS: 0
BUILD TABLE: 1
BUILD INDEX: 0
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 1
TOTAL TIME: 3
Generation 7 (378918238 -> 378844707 nodes, 353899401 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15836902
15 15846215
15 15833117
15 15841862
15 15831233
15 15802789
15 15829781
15 15834851
15 15820176
15 15809725
15 15791766
15 15850618
15 15797398
15 15830803
15 15820985
15 15828480
15 15818443
15 15814121
15 15815820
15 15826174
15 15849595
15 15827581
15 15818803
15 14867469
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
BUILD INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 3
Generation 8 (379004130 -> 378942311 nodes, 364949704 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15843117
15 15849229
15 15835013
15 15846217
15 15833923
15 15806545
15 15833414
15 15837544
15 15823842
15 15812475
15 15794833
15 15852763
15 15803593
15 15834737
15 15824152
15 15832000
15 15821957
15 15818725
15 15821365
15 15830404
15 15854772
15 15831535
15 15823510
15 14876646
FINISHED RECURSIVE SORTS: 0
BUILD TABLE: 0
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 1
TOTAL TIME: 2
Generation 9 (379070273 -> 379023413 nodes, 370753253 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15847114
15 15851330
15 15837089
15 15849111
15 15836805
15 15809421
15 15833971
15 15839979
15 15827632
15 15813893
15 15796572
15 15854573
15 15810862
15 15836648
15 15825876
15 15833737
15 15825282
15 15821444
15 15824968
15 15834352
15 15858904
15 15835078
15 15830587
15 14888185
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
BUILD INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 1
TOTAL TIME: 2
Generation 10 (379138588 -> 379094553 nodes, 374045257 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15849630
15 15852461
15 15839158
15 15849903
15 15837467
15 15811944
15 15834757
15 15842910
15 15830131
15 15814372
15 15797229
15 15855723
15 15816584
15 15837764
15 15826991
15 15836026
15 15826806
15 15823392
15 15827552
15 15836891
15 15864022
15 15838896
15 15839143
15 14904801
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
BUILD INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 0
TOTAL TIME: 2
Generation 11 (379197024 -> 379150175 nodes, 376054726 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15849657
15 15851569
15 15842214
15 15849312
15 15837371
15 15813464
15 15834934
15 15843930
15 15830994
15 15816530
15 15798334
15 15856196
15 15819013
15 15838088
15 15826038
15 15836063
15 15829113
15 15827131
15 15829326
15 15839727
15 15869384
15 15841797
15 15846073
15 14923917
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
BUILD INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 1
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 1
TOTAL TIME: 3
Generation 12 (379238581 -> 379187140 nodes, 377436170 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15849704
15 15850092
15 15844927
15 15849312
15 15837371
15 15815512
15 15833787
15 15843319
15 15831290
15 15818578
15 15798650
15 15856416
15 15816975
15 15838088
15 15826029
15 15834860
15 15831312
15 15833048
15 15831508
15 15843653
15 15874362
15 15842113
15 15853185
15 14933049
FINISHED RECURSIVE SORTS: 0
BUILD TABLE: 0
BUILD INDEX: 0
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 1
TOTAL TIME: 2
Generation 13 (379279715 -> 379232727 nodes, 378492635 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15849117
15 15850092
15 15845913
15 15849312
15 15837371
15 15815650
15 15833745
15 15843319
15 15827557
15 15822674
15 15798650
15 15856416
15 15814099
15 15838088
15 15826029
15 15834860
15 15834717
15 15843359
15 15832263
15 15849372
15 15881492
15 15845096
15 15856585
15 14946951
FINISHED RECURSIVE SORTS: 0
BUILD TABLE: 0
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 1
TOTAL TIME: 2
Generation 14 (379304138 -> 379248130 nodes, 379116739 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15845597
15 15850092
15 15845913
15 15849312
15 15837371
15 15811428
15 15833745
15 15843319
15 15826941
15 15830866
15 15798650
15 15856416
15 15814099
15 15838088
15 15826029
15 15834860
15 15834717
15 15851376
15 15832143
15 15857564
15 15881492
15 15841582
15 15849248
15 14957282
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
BUILD INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 1
TOTAL TIME: 2
Generation 15 (379273989 -> 379258951 nodes, 379258951 ranks)
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 15845597
15 15850092
15 15845913
15 15849312
15 15837371
15 15811428
15 15833745
15 15843319
15 15826941
15 15831596
15 15798650
15 15856416
15 15814099
15 15838088
15 15826029
15 15834860
15 15834717
15 15858880
15 15827425
15 15865068
15 15881492
15 15841582
15 15846763
15 14959568
FINISHED RECURSIVE SORTS: 0
Generating edges... 
NODE.TO -> GENOME POS: 1
BUILD FROM_INDEX 0
COUNTED NEW EDGES: 0
MADE NEW EDGES: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
13 5145698
13 5209447
12 4971812
13 4970724
13 4877756
13 4879699
13 4959696
14 4997234
14 4895059
16 5016287
16 4836997
17 5031595
16 4864028
15 5029532
15 4878030
14 4795112
16 5027465
16 4977115
16 4817515
18 4869154
17 4633311
17 4596500
19 4821801
16 4365134
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 3111634
14 3066522
15 3092346
13 3037703
13 3081077
12 3048241
14 3100037
14 3179284
15 3079689
15 2979297
15 3060897
15 3038285
16 2985406
19 2950944
19 2957967
20 2988169
18 3054934
17 2997902
14 3133981
13 2887471
13 2909073
15 2938340
14 2906533
14 2617750
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
14 3120163
15 3096982
16 3098963
16 3113109
14 3224005
15 3136592
15 3039712
16 3067324
16 3110024
15 3127243
14 3023216
15 3106668
14 2935184
15 2958436
15 3125433
15 3040753
15 3000679
14 2854105
16 2928898
16 2865514
15 2913952
15 2781333
16 2827017
15 2697145
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
22 4992917
22 5029731
21 5067838
23 4963491
20 5123038
16 5076166
15 5031528
15 5071845
15 5102054
15 5094208
14 4951268
13 4800999
14 4933004
13 4963961
13 4931507
13 4767397
13 4858477
13 4961220
13 4834722
13 4644695
12 4705053
11 4659037
12 4767822
11 4228802
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
16 16777216
16 16777216
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15728640
15 15403079
FINISHED RECURSIVE SORTS: 1
RE-SORTED NODES: 2
PROCESS EDGES: 0
REMOVE Y: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
16 16778157
16 16779732
15 15730735
15 15740848
15 15759435
15 15734741
15 15730547
15 15731897
15 15741153
15 15749923
15 15736734
15 15751477
15 15733208
15 15733867
15 15737978
15 15735122
15 15731434
15 15731133
15 15730236
15 15729698
15 15729851
15 15730205
15 15730703
15 15404600
FINISHED RECURSIVE SORTS: 1
SORT, Make index: 1
TOTAL: 7
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/17-Ptuh-lncRNA/genome.index.1.ht2
Wrote 94814744 bytes to secondary GFM file: ../output/17-Ptuh-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/17-Ptuh-lncRNA/genome.index.5.ht2
Wrote 96078770 bytes to secondary GFM file: ../output/17-Ptuh-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: 00:02:46