Settings:
  Output files: "Pocillopora_acuta_HIv2.*.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:
  /gscratch/srlab/sam/data/P_acuta/genomes/Pocillopora_acuta_HIv2.assembly.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: 00:00:02
  Time to read SNPs and splice sites: 00:00:02
Generation 0 (408460640 -> 408460640 nodes, 0 ranks)
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 1
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 1 (408633745 -> 408633745 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 2 (408979967 -> 408979967 nodes, 0 ranks)
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 3 (409672797 -> 409672797 nodes, 0 ranks)
BUILT FROM_INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 1
RESIZE NODES: 5
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
1 17846501
2 16800953
1 11713221
6 12614925
2 10164183
6 12763589
2 11684571
6 14631746
2 18864578
37 9318656
2 10802586
6 12408424
3 9913803
8 11456254
6 9935057
2 14548827
37 9198852
2 9424811
6 11477869
3 10322616
7 10849297
6 9785666
2 9266376
1 8052028
37 9985031
2 10229213
1 8268118
5 8591601
2 8536016
1 7894591
5 8587075
2 10402840
1 8305849
5 9996581
1 9212272
1 9329500
1 17878358
0 0
62 1
84 1
FINISHED RECURSIVE SORTS: 3
SORT NODES: 3
MERGE, UPDATE RANK: 8
Generation 4 (411062436 -> 410376194 nodes, 247885929 ranks)
ALLOCATE FROM_TABLE: 2
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10538197
10 10546445
10 10555816
10 10540201
10 10554548
10 10558405
10 10545291
10 10535010
10 10530328
10 10541936
10 10544101
10 10533306
10 10525640
10 10545240
10 10538047
10 10549951
10 10514870
10 10542756
10 10543174
10 10533806
10 10515313
10 10549427
10 10540536
10 10542642
10 10530945
10 10557999
10 10544084
10 10540329
10 10541155
10 10538491
9 9474693
9 9480779
9 9491122
9 9499469
9 9481549
9 9469368
9 9469190
9 9497052
9 9477462
9 8817521
FINISHED RECURSIVE SORTS: 1
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: 6
TOTAL TIME: 13
Generation 5 (410874488 -> 410453919 nodes, 320409817 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10539066
10 10547303
10 10555751
10 10542697
10 10556354
10 10560333
10 10546376
10 10536318
10 10531947
10 10544982
10 10545438
10 10534833
10 10527249
10 10546657
10 10539758
10 10552409
10 10517456
10 10543649
10 10545118
10 10535215
10 10518186
10 10549523
10 10544360
10 10545827
10 10534663
10 10558827
10 10545996
10 10543018
10 10541966
10 10539778
9 9476330
9 9482454
9 9492801
9 9499918
9 9483786
9 9474339
9 9476869
9 9497537
9 9478897
9 8819935
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 4
TOTAL TIME: 8
Generation 6 (410702051 -> 410619723 nodes, 352700040 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10542127
10 10550411
10 10557802
10 10546711
10 10561535
10 10564086
10 10549942
10 10539461
10 10535416
10 10550490
10 10549578
10 10538596
10 10530395
10 10549503
10 10543099
10 10557862
10 10522098
10 10547014
10 10549409
10 10538948
10 10522421
10 10551937
10 10550998
10 10551229
10 10540328
10 10561773
10 10549808
10 10547824
10 10545146
10 10542957
9 9479523
9 9486488
9 9497441
9 9502795
9 9488327
9 9481850
9 9487128
9 9499756
9 9482487
9 8825024
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 3
TOTAL TIME: 7
Generation 7 (410862661 -> 410776018 nodes, 377409472 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10544995
10 10552862
10 10559592
10 10550119
10 10566647
10 10567748
10 10552807
10 10541895
10 10538182
10 10555740
10 10554192
10 10541875
10 10533495
10 10552352
10 10545922
10 10562866
10 10526479
10 10549842
10 10553911
10 10542843
10 10526977
10 10553686
10 10557778
10 10555596
10 10545785
10 10564081
10 10553701
10 10552015
10 10548038
10 10545940
9 9482726
9 9490319
9 9502206
9 9504866
9 9492772
9 9490199
9 9497660
9 9501094
9 9486002
9 8830213
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
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: 6
Generation 8 (410980359 -> 410901116 nodes, 393337097 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10548468
10 10554395
10 10560572
10 10552413
10 10569900
10 10570796
10 10554976
10 10542930
10 10540865
10 10560530
10 10558995
10 10543645
10 10535845
10 10554740
10 10547829
10 10567366
10 10529904
10 10551903
10 10556695
10 10546393
10 10531222
10 10555064
10 10562874
10 10558322
10 10550550
10 10566210
10 10556657
10 10554559
10 10550681
10 10548900
9 9485397
9 9492565
9 9505261
9 9506377
9 9496715
9 9497933
9 9507309
9 9503020
9 9488369
9 8833971
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
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: 6
Generation 9 (411059729 -> 410991884 nodes, 401980396 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 10551923
10 10555470
10 10560712
10 10554489
10 10572163
10 10571894
10 10556872
10 10543254
10 10543259
10 10564235
10 10563019
10 10544988
10 10536905
10 10556070
10 10549215
10 10571569
10 10531953
10 10553281
10 10559689
10 10548593
10 10532778
10 10556700
10 10566737
10 10560392
10 10553093
10 10568080
10 10558307
10 10556016
10 10552002
10 10552121
9 9487110
9 9494231
9 9507923
9 9507088
9 9499653
9 9504853
9 9515411
9 9503870
9 9489146
9 8836820
FINISHED RECURSIVE SORTS: 2
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 7
Generation 10 (411111015 -> 411055497 nodes, 406073542 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10553236
10 10556560
10 10560805
10 10554426
10 10572355
10 10572227
10 10556863
10 10543300
10 10546295
10 10564705
10 10565821
10 10546465
10 10536998
10 10555385
10 10550748
10 10574078
10 10533690
10 10554359
10 10562508
10 10552110
10 10533030
10 10557815
10 10569182
10 10563284
10 10555741
10 10570970
10 10558674
10 10555689
10 10553687
10 10553790
9 9487837
9 9496221
9 9508040
9 9506863
9 9502855
9 9507876
9 9526380
9 9504818
9 9489794
9 8840017
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 2
TOTAL TIME: 8
Generation 11 (411150227 -> 411107306 nodes, 408215124 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10553778
10 10558819
10 10560805
10 10555371
10 10572665
10 10572353
10 10557007
10 10543300
10 10548364
10 10563444
10 10567695
10 10547620
10 10537992
10 10554983
10 10552714
10 10574497
10 10535534
10 10554129
10 10565030
10 10555339
10 10532732
10 10558281
10 10570344
10 10567641
10 10559354
10 10574238
10 10558394
10 10555845
10 10555363
10 10553530
9 9489154
9 9499132
9 9507773
9 9506681
9 9504575
9 9507257
9 9537634
9 9504818
9 9489822
9 8843299
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 1
MERGEUPDATERANK: 1
TOTAL TIME: 7
Generation 12 (411182953 -> 411147879 nodes, 409772806 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
10 10553943
10 10558463
10 10560805
10 10557419
10 10572285
10 10571891
10 10557007
10 10543300
10 10549499
10 10563444
10 10568324
10 10549668
10 10538383
10 10554983
10 10554271
10 10574646
10 10537860
10 10554129
10 10565968
10 10560170
10 10532732
10 10558281
10 10569666
10 10570383
10 10564600
10 10575230
10 10558394
10 10555845
10 10557153
10 10552489
9 9489534
9 9503228
9 9507773
9 9506681
9 9508671
9 9504574
9 9545450
9 9504818
9 9489822
9 8846097
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 2
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 2
TOTAL TIME: 8
Generation 13 (411190675 -> 411169099 nodes, 410805169 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10553943
10 10558463
10 10560805
10 10557470
10 10572285
10 10571891
10 10557007
10 10543300
10 10545704
10 10563442
10 10568239
10 10550730
10 10538383
10 10554983
10 10554271
10 10574646
10 10535403
10 10554129
10 10570064
10 10561283
10 10532732
10 10558281
10 10569666
10 10573395
10 10566451
10 10575230
10 10558394
10 10555845
10 10556825
10 10552489
9 9489534
9 9507819
9 9507773
9 9506681
9 9511608
9 9504574
9 9552593
9 9504818
9 9489822
9 8848128
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 2
TOTAL TIME: 7
Generation 14 (411186951 -> 411164090 nodes, 411153616 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10553943
10 10558463
10 10560805
10 10557470
10 10572285
10 10571891
10 10557007
10 10543300
10 10545704
10 10563442
10 10568239
10 10550730
10 10538383
10 10554983
10 10554271
10 10574646
10 10535402
10 10554129
10 10573212
10 10557340
10 10532732
10 10558281
10 10569666
10 10573394
10 10566451
10 10575230
10 10558394
10 10555845
10 10556825
10 10552489
9 9489534
9 9508964
9 9507773
9 9506681
9 9511608
9 9504574
9 9547236
9 9504818
9 9489822
9 8848128
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 2
BUILD INDEX: 1
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 0
RESIZED NODES: 0
MADE NEW NODES: 0
MERGEUPDATERANK: 2
TOTAL TIME: 6
Generation 15 (411164090 -> 411162272 nodes, 411162272 ranks)
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 10553943
10 10558463
10 10560805
10 10557470
10 10572285
10 10571891
10 10557007
10 10543300
10 10545704
10 10563442
10 10568239
10 10550730
10 10538383
10 10554983
10 10554271
10 10574646
10 10535402
10 10554129
10 10573212
10 10557340
10 10532732
10 10558281
10 10569666
10 10573394
10 10566451
10 10575230
10 10558394
10 10555845
10 10556825
10 10552489
9 9489534
9 9508964
9 9507773
9 9506681
9 9511608
9 9504574
9 9545418
9 9504818
9 9489822
9 8848128
FINISHED RECURSIVE SORTS: 2
Generating edges... 
NODE.TO -> GENOME POS: 1
BUILD FROM_INDEX 1
COUNTED NEW EDGES: 1
MADE NEW EDGES: 2
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
8 3225339
9 3498320
8 3265229
9 3550911
8 3434381
9 3500082
9 3222965
9 3442674
9 3294509
9 3412193
9 3468124
9 3141033
9 3338875
9 3213354
10 3232871
10 3125029
10 3117790
11 3279512
11 3319164
11 3212055
11 3248393
10 3331022
10 3313896
10 3237278
9 3073932
9 3035314
10 3156222
10 3151206
10 3131634
10 2927343
10 3087040
10 2995164
12 3097309
11 2982122
11 3015933
11 2949331
11 2940977
12 2963835
10 2723751
10 2511854
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 2064218
10 2129987
9 1975358
10 2123877
10 2053117
9 2110379
9 2099952
9 2181361
8 1946445
8 1975452
9 1991986
9 2116600
9 2005181
10 2026338
10 2057760
10 2005373
10 2119954
10 1915715
10 1972260
10 2093667
10 1916772
13 1999941
12 1864503
11 1871574
14 1976424
12 1872395
12 1862771
11 1968658
11 1930606
11 1992372
8 1859001
8 1842917
9 1992420
8 1792484
8 1788609
10 1878525
9 1904576
9 1864799
9 1778330
9 1509404
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
9 2002761
9 1961537
10 2025546
10 2030062
11 2131823
10 1991507
10 2048159
9 1966254
9 2028909
10 2064596
10 2079649
10 1936602
11 2096872
10 1995730
11 2154521
10 2074854
9 1954417
9 2001110
10 2101447
10 2030542
9 1928293
10 2000278
10 1951064
10 2061204
9 1898827
10 2032764
10 2025853
10 1953850
9 1831571
10 2005572
10 1910238
11 1929362
11 1971975
10 1948733
9 1734868
10 1866021
10 1698973
9 1667542
10 1817434
9 1515605
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
15 3322056
15 3365219
14 3239582
13 3331965
14 3180687
16 3292011
13 3211480
13 3248894
11 3167061
10 3286601
10 3338086
10 3353468
10 3366501
10 3358706
10 3393307
10 3382945
9 3132572
9 3198860
9 3382884
9 3132061
9 3153089
9 3303527
8 3089804
9 3327716
8 3102998
9 3220791
9 3376017
8 3008077
8 3010307
8 3089672
8 3133600
9 3124272
9 3202367
8 3049049
8 3182946
7 3002731
7 2874497
8 3172062
7 2731037
7 2470653
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 3
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 8509088
FINISHED RECURSIVE SORTS: 1
RE-SORTED NODES: 4
PROCESS EDGES: 1
REMOVE Y: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 10486241
10 10486504
10 10487531
10 10486905
10 10487397
10 10496419
10 10492165
10 10503288
10 10501872
10 10487016
10 10487119
10 10486938
10 10488157
10 10495489
10 10491033
10 10500451
10 10493920
10 10491750
10 10501061
10 10497035
10 10488742
10 10489828
10 10488428
10 10491342
10 10493266
10 10488419
10 10489255
10 10486229
10 10488207
10 10486217
10 10487061
10 10486478
10 10486422
9 9437985
9 9437884
9 9438102
9 9438234
9 9438729
9 9438091
9 8509901
FINISHED RECURSIVE SORTS: 1
SORT, Make index: 4
TOTAL: 18
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 127167966
fchr[G]: 205600027
fchr[T]: 284026952
fchr[$]: 411337110
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 257350077 bytes to primary GFM file: Pocillopora_acuta_HIv2.1.ht2
Wrote 102790572 bytes to secondary GFM file: Pocillopora_acuta_HIv2.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 279216699 bytes to primary GFM file: Pocillopora_acuta_HIv2.5.ht2
Wrote 104130710 bytes to secondary GFM file: Pocillopora_acuta_HIv2.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 408287534
    gbwtLen: 411337111
    nodes: 411162271
    sz: 204143767
    gbwtSz: 205668556
    lineRate: 7
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 25697642
    offsSz: 102790568
    lineSz: 128
    sideSz: 128
    sideGbwtSz: 104
    sideGbwtLen: 208
    numSides: 1977583
    numLines: 1977583
    gbwtTotLen: 253130624
    gbwtTotSz: 253130624
    reverse: 0
    linearFM: No
Total time for call to driver() for forward index: 00:07:22