Settings:
  Output files: "../output/06-Ptua-lncRNA-discovery/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/06-Ptua-lncRNA-discovery/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: 00:00:00
  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: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 1
RESIZED NODES: 0
MADE NEW NODES: 0
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: 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
2 15540590
1 10832317
6 11628773
2 9368794
6 11772948
2 10804545
5 7614352
2 12496986
1 10854948
37 8605401
2 9941984
6 11457454
3 9114572
7 7405416
6 7443549
2 10115785
1 8080675
37 8494430
2 8697179
6 10580945
3 9426625
6 7227238
2 6738255
6 8945362
2 12043997
37 9261921
2 9424175
1 7627115
5 7971358
2 7844988
1 7302015
5 7944966
1 4692016
1 4853501
1 7655401
5 9274166
1 8506986
1 8603410
1 16518930
0 0
0 0
2 1
16 1
46 1
82 1
FINISHED RECURSIVE SORTS: 1
SORT NODES: 1
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
8 8451147
8 8422582
8 8456966
8 8432148
8 8440481
8 8440960
8 8443829
8 8447710
8 8438942
8 8415926
8 8425306
8 8420200
8 8442995
8 8434538
8 8445441
8 8437207
8 8429149
8 8436216
8 8403747
8 8412138
8 8437609
8 8448404
8 8433537
8 8407656
8 8436847
8 8439238
8 8435274
8 8429836
8 8434843
8 8436628
8 8429805
8 8432384
8 8428175
8 8420244
8 8417000
8 8444952
8 8428853
8 8442928
7 7384771
7 7382357
7 7377702
7 7389230
7 7376720
7 7370656
7 7346926
7 6444613
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: 3
TOTAL TIME: 5
Generation 5 (378979682 -> 378592021 nodes, 307454446 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
8 8450872
8 8425028
8 8457635
8 8432793
8 8440748
8 8441842
8 8445915
8 8448602
8 8439139
8 8419737
8 8426517
8 8421372
8 8442624
8 8436031
8 8445617
8 8438512
8 8429697
8 8437437
8 8406188
8 8414110
8 8438775
8 8450105
8 8434217
8 8409518
8 8437174
8 8439384
8 8436210
8 8430752
8 8435951
8 8436963
8 8430452
8 8434040
8 8430263
8 8423012
8 8419480
8 8445579
8 8430325
8 8443719
7 7385906
7 7383158
7 7378651
7 7390662
7 7377774
7 7371262
7 7349628
7 6448645
FINISHED RECURSIVE SORTS: 0
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
8 8453320
8 8429796
8 8460718
8 8434530
8 8443044
8 8444579
8 8449827
8 8451700
8 8441199
8 8424292
8 8428920
8 8423735
8 8445110
8 8439981
8 8447696
8 8441458
8 8431635
8 8440382
8 8409414
8 8417036
8 8441737
8 8453463
8 8436584
8 8412662
8 8439377
8 8441673
8 8439129
8 8433216
8 8438731
8 8439626
8 8432513
8 8436809
8 8434117
8 8427077
8 8423098
8 8448920
8 8433529
8 8446887
7 7389147
7 7385399
7 7380948
7 7393655
7 7380310
7 7373403
7 7353007
7 6454116
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
8 8456012
8 8434684
8 8463207
8 8435945
8 8444264
8 8446801
8 8453080
8 8453787
8 8442624
8 8429055
8 8430702
8 8425614
8 8447704
8 8443865
8 8449406
8 8443313
8 8433482
8 8442859
8 8411876
8 8419102
8 8444378
8 8455816
8 8438694
8 8415613
8 8441255
8 8443766
8 8441409
8 8435103
8 8441389
8 8441896
8 8434186
8 8438632
8 8436852
8 8430759
8 8426768
8 8451816
8 8436637
8 8449604
7 7392220
7 7387177
7 7383081
7 7396039
7 7382455
7 7375200
7 7357286
7 6459294
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 8 (379004130 -> 378942311 nodes, 364949704 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
8 8458139
8 8439074
8 8465313
8 8436928
8 8444996
8 8448168
8 8456303
8 8455000
8 8444061
8 8432061
8 8432106
8 8426816
8 8450024
8 8445552
8 8450461
8 8444583
8 8435878
8 8444552
8 8413187
8 8420105
8 8446212
8 8457320
8 8441202
8 8419441
8 8443251
8 8445427
8 8443465
8 8436711
8 8443074
8 8443987
8 8436455
8 8439894
8 8438795
8 8434280
8 8429677
8 8454074
8 8438886
8 8452246
7 7395081
7 7388664
7 7384832
7 7398407
7 7384009
7 7377891
7 7362269
7 6463454
FINISHED RECURSIVE SORTS: 0
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 9 (379070273 -> 379023413 nodes, 370753253 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
8 8459344
8 8442343
8 8466386
8 8437781
8 8445983
8 8449419
8 8458210
8 8456161
8 8445882
8 8434226
8 8433257
8 8427113
8 8450077
8 8446837
8 8451801
8 8445369
8 8438882
8 8445550
8 8413834
8 8420508
8 8446982
8 8458716
8 8444257
8 8423396
8 8444697
8 8445985
8 8444899
8 8437860
8 8443572
8 8445286
8 8438508
8 8441166
8 8440080
8 8436781
8 8432156
8 8454416
8 8441120
8 8454985
7 7396705
7 7389526
7 7386516
7 7400785
7 7386871
7 7381833
7 7368515
7 6468837
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
8 8460016
8 8443945
8 8467759
8 8438293
8 8446516
8 8450185
8 8458748
8 8457185
8 8446130
8 8435308
8 8434600
8 8427521
8 8450455
8 8448264
8 8453305
8 8445548
8 8441202
8 8446612
8 8413251
8 8421225
8 8446892
8 8459995
8 8445792
8 8425959
8 8446525
8 8445333
8 8446668
8 8438671
8 8444633
8 8446514
8 8439429
8 8441769
8 8440417
8 8439011
8 8434186
8 8453876
8 8442478
8 8457542
7 7398373
7 7392061
7 7387415
7 7403281
7 7390916
7 7386781
7 7378647
7 6475321
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: 0
TOTAL TIME: 2
Generation 11 (379197024 -> 379150175 nodes, 376054726 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
8 8458281
8 8445707
8 8467265
8 8438490
8 8446929
8 8452233
8 8457778
8 8457908
8 8445690
8 8435385
8 8436043
8 8427698
8 8450455
8 8448693
8 8453896
8 8445533
8 8442080
8 8447806
8 8414215
8 8422400
8 8446807
8 8460483
8 8447911
8 8426548
8 8446181
8 8445333
8 8446121
8 8438654
8 8445212
8 8445972
8 8440280
8 8443225
8 8441402
8 8441765
8 8435960
8 8453876
8 8444106
8 8459425
7 7399776
7 7395345
7 7388640
7 7404842
7 7394116
7 7390626
7 7390588
7 6482496
FINISHED RECURSIVE SORTS: 0
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
8 8457936
8 8446099
8 8465788
8 8438490
8 8448977
8 8452898
8 8457778
8 8457908
8 8445690
8 8435385
8 8438091
8 8426551
8 8450455
8 8448082
8 8453896
8 8445533
8 8442376
8 8447806
8 8416263
8 8422716
8 8446807
8 8460703
8 8447454
8 8425522
8 8445626
8 8445333
8 8446112
8 8438654
8 8445212
8 8444769
8 8440431
8 8445273
8 8441175
8 8447909
8 8438142
8 8453876
8 8445984
8 8460846
7 7403170
7 7397556
7 7390688
7 7403110
7 7396434
7 7395420
7 7398118
7 6484098
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 13 (379279715 -> 379232727 nodes, 378492635 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
8 8457936
8 8445512
8 8465788
8 8438490
8 8449963
8 8452898
8 8457778
8 8457908
8 8445690
8 8435385
8 8438229
8 8426509
8 8450455
8 8448082
8 8453896
8 8445533
8 8438643
8 8447806
8 8420359
8 8422716
8 8446807
8 8460703
8 8444578
8 8425522
8 8445626
8 8445333
8 8446112
8 8438654
8 8445212
8 8444769
8 8440431
8 8448678
8 8441175
8 8458220
8 8438897
8 8453876
8 8447607
8 8464134
7 7411108
7 7397556
7 7393671
7 7403110
7 7393089
7 7402165
7 7408187
7 6487931
FINISHED RECURSIVE SORTS: 0
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 14 (379304138 -> 379248130 nodes, 379116739 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
8 8457936
8 8441992
8 8465788
8 8438490
8 8449963
8 8452898
8 8457778
8 8457908
8 8445690
8 8435385
8 8434007
8 8426509
8 8450455
8 8448082
8 8453896
8 8445533
8 8438027
8 8447806
8 8428551
8 8422716
8 8446807
8 8460703
8 8444578
8 8425522
8 8445626
8 8445333
8 8446112
8 8438654
8 8445212
8 8444769
8 8440431
8 8448678
8 8441175
8 8466237
8 8438777
8 8453876
8 8447607
8 8472326
7 7411108
7 7397556
7 7393671
7 7399596
7 7393089
7 7394828
7 7425394
7 6481055
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: 0
TOTAL TIME: 1
Generation 15 (379273989 -> 379258951 nodes, 379258951 ranks)
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
8 8457936
8 8441992
8 8465788
8 8438490
8 8449963
8 8452898
8 8457778
8 8457908
8 8445690
8 8435385
8 8434007
8 8426509
8 8450455
8 8448082
8 8453896
8 8445533
8 8438027
8 8447806
8 8429281
8 8422716
8 8446807
8 8460703
8 8444578
8 8425522
8 8445626
8 8445333
8 8446112
8 8438654
8 8445212
8 8444769
8 8440431
8 8448678
8 8441175
8 8473741
8 8434059
8 8453876
8 8447607
7 7424899
8 8466039
7 7397556
7 7393671
7 7399596
7 7390604
7 7394828
7 7430505
7 6478230
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: 1
FINISHED FIRST ROUND: 0
7 2824571
7 2717595
7 2831525
7 2767485
7 2888373
7 2938899
7 2627403
7 2516121
7 2689957
7 2598346
7 2654861
7 2638476
7 2659617
8 2775987
7 2624694
7 2487652
8 2648298
8 2483467
8 2499590
9 2712354
9 2698638
9 2712763
9 2649767
9 2665429
8 2702645
8 2671051
8 2574183
8 2636602
7 2450116
8 2642132
8 2485274
8 2549329
8 2506868
8 2392700
8 2372054
8 2488109
9 2447280
9 2334804
9 2504471
9 2455183
9 2420374
8 2196022
9 2183209
9 2338029
7 1948459
7 1855939
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
8 1630758
8 1683980
8 1752922
8 1742896
8 1614878
8 1706583
7 1700746
7 1617702
7 1666286
7 1715887
6 1604885
8 1644747
7 1675083
7 1597756
7 1589169
8 1595029
8 1644688
8 1641321
8 1647866
8 1613815
9 1702869
8 1710536
8 1605519
9 1611626
10 1526163
10 1567652
9 1524658
11 1558564
11 1592984
10 1575265
9 1491509
8 1449178
9 1557454
8 1449581
7 1520834
7 1643782
7 1534823
7 1592045
7 1526929
7 1527884
8 1475510
6 1280753
7 1476857
7 1374049
6 1208609
6 1030852
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
8 1776482
7 1565696
9 1749308
8 1729703
9 1702067
8 1575085
8 1570541
8 1725618
8 1750191
7 1569354
8 1649881
8 1635996
8 1653017
9 1647694
8 1596217
8 1581215
8 1528809
8 1695020
8 1654784
7 1540165
8 1656526
7 1517039
8 1648919
8 1652948
8 1635042
8 1536258
8 1649455
8 1590476
7 1505663
8 1616085
8 1620450
8 1587289
7 1434656
7 1444586
8 1460959
8 1503306
9 1537438
8 1479065
8 1538083
8 1553801
8 1477592
8 1450727
8 1382167
7 1305549
7 1275369
7 1236159
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
12 2664250
11 2564568
12 2614197
11 2676283
10 2559130
12 2628325
13 2674613
11 2708166
11 2715644
10 2836332
8 2572236
8 2683345
8 2740237
8 2636964
8 2743542
8 2682916
8 2757860
8 2664676
8 2783919
7 2599046
8 2782913
7 2677339
8 2687561
7 2536790
7 2535736
7 2701105
7 2558424
7 2784902
7 2460160
7 2669773
7 2563694
7 2658225
7 2709932
7 2677876
6 2334422
7 2413785
7 2485070
7 2578172
6 2391845
6 2422792
5 2154086
5 2059441
6 2417401
5 1958222
6 2292045
4 1542820
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
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 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 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
8 8388608
7 7340032
7 7340032
7 7340032
7 7340032
7 7340032
7 7014471
FINISHED RECURSIVE SORTS: 1
RE-SORTED NODES: 2
PROCESS EDGES: 0
REMOVE Y: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
8 8388963
8 8389194
8 8389482
8 8390250
8 8389135
8 8390432
8 8398089
8 8393488
8 8400506
8 8407663
8 8391609
8 8389643
8 8389573
8 8389620
8 8390585
8 8396337
8 8393415
8 8395152
8 8404032
8 8391250
8 8395516
8 8401280
8 8397804
8 8391117
8 8391487
8 8391479
8 8391113
8 8394260
8 8394338
8 8390858
8 8391422
8 8389293
8 8390287
8 8389449
8 8389749
8 8389133
8 8389201
8 8389118
8 8389291
8 8389263
7 7340763
7 7340837
7 7340937
7 7341064
7 7340809
7 7015128
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/06-Ptua-lncRNA-discovery/genome.index.1.ht2
Wrote 94814744 bytes to secondary GFM file: ../output/06-Ptua-lncRNA-discovery/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/06-Ptua-lncRNA-discovery/genome.index.5.ht2
Wrote 96078770 bytes to secondary GFM file: ../output/06-Ptua-lncRNA-discovery/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