Settings:
  Output files: "../output/01-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-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: 00:00:06
  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: 1
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 1 (376906272 -> 376906272 nodes, 0 ranks)
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 2 (377232638 -> 377232638 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 1
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 3 (377885652 -> 377885652 nodes, 0 ranks)
BUILT FROM_INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 1
RESIZED NODES: 0
MADE NEW NODES: 0
RESIZE NODES: 2
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
4 42853232
16 43575060
45 39571687
18 37919426
47 38042472
18 38762209
46 35289471
10 35131460
13 34420050
149 33629330
FINISHED RECURSIVE SORTS: 3
SORT NODES: 3
MERGE, UPDATE RANK: 4
Generation 4 (379194397 -> 378534816 nodes, 240705876 ranks)
ALLOCATE FROM_TABLE: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
36 37977374
36 37997391
36 37922559
36 37964419
36 37922122
36 37932328
36 37945632
36 37928235
36 37959770
36 36984986
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 2
BUILD INDEX: 0
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 2
MERGEUPDATERANK: 3
TOTAL TIME: 8
Generation 5 (378979682 -> 378592021 nodes, 307454446 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
36 37980952
36 38001622
36 37929360
36 37968184
36 37929291
36 37936390
36 37949194
36 37937298
36 37965111
36 36994619
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
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: 5
Generation 6 (378799003 -> 378727505 nodes, 334740479 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
36 37993903
36 38014810
36 37943475
36 37979734
36 37942538
36 37948537
36 37960248
36 37953859
36 37979051
36 37011350
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
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: 4
Generation 7 (378918238 -> 378844707 nodes, 353899401 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
36 38005691
36 38024713
36 37956709
36 37989291
36 37952631
36 37959278
36 37969631
36 37967770
36 37991659
36 37027334
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 2
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: 4
Generation 8 (379004130 -> 378942311 nodes, 364949704 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
36 38015539
36 38032443
36 37965373
36 37996660
36 37958900
36 37970710
36 37977724
36 37979223
36 38002519
36 37043220
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
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: 3
Generation 9 (379070273 -> 379023413 nodes, 370753253 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
36 38022565
36 38038944
36 37969877
36 38003235
36 37962869
36 37980405
36 37983458
36 37986367
36 38011409
36 37064284
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
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: 4
Generation 10 (379138588 -> 379094553 nodes, 374045257 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
36 38026998
36 38041779
36 37973817
36 38008998
36 37964093
36 37987547
36 37987682
36 37990824
36 38020346
36 37092469
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 0
TOTAL TIME: 3
Generation 11 (379197024 -> 379150175 nodes, 376054726 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
36 38026117
36 38044164
36 37975943
36 38011646
36 37966635
36 37989364
36 37988985
36 37997361
36 38029769
36 37120191
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
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: 4
Generation 12 (379238581 -> 379187140 nodes, 377436170 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
36 38024687
36 38046877
36 37976844
36 38011331
36 37969219
36 37987317
36 37987933
36 38007508
36 38040721
36 37134703
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
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: 4
Generation 13 (379279715 -> 379232727 nodes, 378492635 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
36 38024100
36 38047863
36 37976940
36 38007598
36 37973315
36 37984441
36 37987933
36 38021979
36 38056553
36 37152005
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
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: 4
Generation 14 (379304138 -> 379248130 nodes, 379116739 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
36 38020580
36 38047863
36 37972718
36 38006982
36 37981507
36 37984441
36 37987933
36 38029876
36 38064745
36 37151485
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
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: 3
Generation 15 (379273989 -> 379258951 nodes, 379258951 ranks)
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
36 38020580
36 38047863
36 37972718
36 38006982
36 37982237
36 37984441
36 37987933
36 38032662
36 38072249
36 37151286
FINISHED RECURSIVE SORTS: 1
Generating edges... 
NODE.TO -> GENOME POS: 0
BUILD FROM_INDEX 0
COUNTED NEW EDGES: 1
MADE NEW EDGES: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
30 11912242
31 12068183
31 11694860
34 11746985
39 11852287
37 11662968
36 11834600
38 11711254
43 11669794
43 11313528
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
34 7238480
33 7373251
31 7378757
34 7216365
36 7293549
43 7312424
47 7241546
36 7120799
33 7143226
35 6885085
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
35 7382470
36 7323710
35 7300893
37 7233289
34 7216756
36 7335886
36 7281619
37 7191107
38 7088988
38 6837732
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
51 11842446
52 11962730
37 11818517
35 11784763
33 11911575
33 11924304
31 11580902
31 11730134
31 11893051
28 11112358
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 2
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
37 38797312
37 38797312
36 37748736
36 37748736
36 37748736
36 37748736
36 37748736
36 37748736
36 37748736
36 37423175
FINISHED RECURSIVE SORTS: 2
RE-SORTED NODES: 3
PROCESS EDGES: 0
REMOVE Y: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
37 38801097
37 38831800
36 37767387
36 37772472
36 37792623
36 37761311
36 37764422
36 37753186
36 37751650
36 37427466
FINISHED RECURSIVE SORTS: 2
SORT, Make index: 2
TOTAL: 10
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-lncRNA/genome.index.1.ht2
Wrote 94814744 bytes to secondary GFM file: ../output/01-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-lncRNA/genome.index.5.ht2
Wrote 96078770 bytes to secondary GFM file: ../output/01-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: 00:04:11