Settings:
  Output files: "Pver_genome_assembly_v1.0.*.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_verrucosa/genomes/Pver_genome_assembly_v1.0.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: 00:00:04
Generation 0 (380155422 -> 380155422 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 1 (380315179 -> 380315179 nodes, 0 ranks)
COUNTED NEW NODES: 1
COUNTED TEMP NODES: 0
RESIZED NODES: 1
RESIZED NODES: 0
MADE NEW NODES: 1
Generation 2 (380634713 -> 380634713 nodes, 0 ranks)
COUNTED NEW NODES: 0
COUNTED TEMP NODES: 0
RESIZED NODES: 2
RESIZED NODES: 0
MADE NEW NODES: 0
Generation 3 (381273892 -> 381273892 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: 4
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
1 16627568
2 15610124
1 10961036
6 11730911
2 9426418
6 11835923
2 10869417
6 13658126
2 17637744
37 8662864
2 10075069
6 11591449
3 9232871
8 10634020
6 9186506
2 13523988
37 8551470
2 8764709
6 10712353
3 9584109
7 10117288
6 9091926
2 8605407
1 7481366
37 9346133
2 9440792
1 7700076
5 8037983
2 7914724
1 7334955
5 8041394
2 9678715
1 7694460
5 9346868
1 8555248
1 8654852
1 16634288
0 0
45 1
101 1
FINISHED RECURSIVE SORTS: 2
SORT NODES: 3
MERGE, UPDATE RANK: 7
Generation 4 (382553152 -> 381941994 nodes, 257562629 ranks)
ALLOCATE FROM_TABLE: 3
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10559605
10 10564114
10 10545375
9 9501569
9 9496471
9 9497219
9 9492074
9 9501188
9 9498190
9 9496349
9 9494274
9 9496329
9 9491262
9 9494050
9 9492810
9 9492928
9 9491189
9 9487274
9 9492231
9 9490042
9 9494213
9 9493767
9 9488072
9 9487402
9 9490702
9 9482363
9 9481513
9 9480128
9 9476755
9 9475870
9 9468444
9 9462461
9 9458782
9 9453064
9 9442895
9 9475827
9 9471862
9 9467067
9 9484361
9 8831903
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: 2
MERGEUPDATERANK: 4
TOTAL TIME: 12
Generation 5 (382455931 -> 382054748 nodes, 329188033 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10559726
10 10565719
10 10547192
9 9502692
9 9497876
9 9499467
9 9493546
9 9501897
9 9499458
9 9497840
9 9496397
9 9497972
9 9493248
9 9496954
9 9494103
9 9495804
9 9493595
9 9489809
9 9494799
9 9492214
9 9495679
9 9496001
9 9490854
9 9489769
9 9493237
9 9484719
9 9485055
9 9485011
9 9480439
9 9481222
9 9474897
9 9467588
9 9465482
9 9459367
9 9445372
9 9478656
9 9477686
9 9469137
9 9487540
9 8836729
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: 3
TOTAL TIME: 8
Generation 6 (382339836 -> 382235516 nodes, 354994012 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 10563460
10 10570887
10 10551316
9 9507072
9 9501531
9 9504070
9 9496740
9 9505456
9 9503111
9 9501820
9 9500916
9 9501863
9 9497260
9 9501920
9 9497486
9 9500565
9 9497854
9 9494205
9 9499145
9 9495669
9 9499185
9 9500632
9 9494944
9 9494184
9 9498164
9 9488359
9 9489666
9 9491073
9 9485017
9 9487277
9 9481630
9 9472942
9 9472156
9 9466058
9 9448064
9 9482631
9 9484468
9 9471865
9 9492590
9 8842265
FINISHED RECURSIVE SORTS: 1
BUILD TABLE: 1
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: 5
Generation 7 (382490079 -> 382376200 nodes, 371437364 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10566424
10 10575099
10 10554214
9 9511432
9 9504067
9 9508028
9 9499093
9 9508884
9 9506439
9 9505573
9 9504786
9 9504980
9 9500311
9 9505950
9 9500814
9 9504341
9 9501897
9 9496952
9 9502506
9 9498308
9 9501915
9 9504790
9 9497416
9 9497734
9 9501868
9 9490925
9 9493240
9 9495536
9 9488385
9 9490817
9 9486336
9 9476748
9 9477543
9 9471131
9 9449598
9 9485341
9 9489394
9 9473439
9 9496646
9 8847300
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: 2
TOTAL TIME: 6
Generation 8 (382522123 -> 382421917 nodes, 380138761 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 10567172
10 10577326
10 10554511
9 9513891
9 9504900
9 9510037
9 9499766
9 9509990
9 9508537
9 9507352
9 9505742
9 9505657
9 9500772
9 9507866
9 9502025
9 9505966
9 9503709
9 9497014
9 9502899
9 9499244
9 9502643
9 9506390
9 9498258
9 9499521
9 9502526
9 9491528
9 9493957
9 9496806
9 9489789
9 9491910
9 9487561
9 9478161
9 9479205
9 9472452
9 9449335
9 9485728
9 9491667
9 9473699
9 9497832
9 8848573
FINISHED RECURSIVE SORTS: 2
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: 2
TOTAL TIME: 5
Generation 9 (382453480 -> 382401621 nodes, 382355456 ranks)
ALLOCATE FROM_TABLE: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 10566660
10 10576185
10 10553733
9 9513185
9 9504331
9 9509627
9 9499223
9 9509859
9 9508427
9 9507023
9 9505786
9 9505471
9 9500247
9 9507598
9 9500845
9 9505501
9 9503260
9 9496097
9 9502151
9 9498819
9 9502103
9 9506148
9 9497681
9 9498630
9 9501732
9 9490963
9 9493616
9 9496676
9 9490018
9 9491638
9 9486942
9 9476957
9 9478531
9 9472456
9 9449093
9 9484958
9 9491065
9 9473486
9 9497064
9 8847836
FINISHED RECURSIVE SORTS: 2
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: 1
TOTAL TIME: 4
Generation 10 (382402327 -> 382399107 nodes, 382399107 ranks)
COUNT NUMBER IN EACH BIN: 1
FINISHED FIRST ROUND: 0
10 10566660
10 10575850
10 10553733
9 9512911
9 9504172
9 9509635
9 9499136
9 9509859
9 9508343
9 9506998
9 9505846
9 9505407
9 9500247
9 9507586
9 9500809
9 9505504
9 9503359
9 9495929
9 9502071
9 9498757
9 9502033
9 9505877
9 9497659
9 9498491
9 9501502
9 9490847
9 9493565
9 9496614
9 9490007
9 9491661
9 9486942
9 9476941
9 9478486
9 9472377
9 9449093
9 9484879
9 9491065
9 9473486
9 9496962
9 8847808
FINISHED RECURSIVE SORTS: 1
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 3224060
8 3122571
8 3245091
8 3168521
7 2996264
8 3125252
9 3234249
8 3061732
8 2940767
8 3036034
8 3089673
9 3164666
8 2981227
9 3227310
9 2934444
10 3081402
10 3083453
10 3014025
10 3000194
10 2920537
10 2946796
9 3018610
9 2969132
9 2903977
9 3016952
9 3045427
9 2844434
9 2826121
9 2831162
10 2956097
9 2778842
10 3013394
11 2834340
10 2729748
10 2753468
10 2692752
10 2704783
11 2708762
10 2729837
9 2401649
FINISHED RECURSIVE SORTS: 1
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
9 1842150
9 1917213
9 1969965
9 1914510
9 1830024
8 1857319
8 1907689
8 1867591
8 1999899
7 1814765
9 1942912
8 1886442
9 2008244
9 1850426
9 1858635
9 1849703
9 1835713
9 1789354
10 1924986
9 1910841
9 1873062
12 1773107
12 1888987
11 1851106
13 1846584
12 1862285
12 1864861
10 1793871
10 1708626
10 1834129
8 1865490
8 1814856
8 1798238
8 1787907
8 1740589
9 1685317
8 1692584
8 1631467
8 1590300
7 1223599
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
9 1994882
9 1927809
9 1845054
10 1998892
10 1940487
10 1972579
9 1935380
9 2002294
9 1912368
9 1850618
9 1927366
10 1822554
9 1786075
9 1783093
10 1974640
9 1869215
9 1980744
9 1912830
9 1919170
9 1859493
9 1816037
9 1819418
9 1816580
9 1855330
9 1865300
9 1847448
9 1815550
9 1797632
9 1802449
9 1794081
9 1715717
10 1717000
10 1821422
9 1746177
9 1716601
9 1689362
10 1675223
8 1516658
8 1431880
8 1430818
FINISHED RECURSIVE SORTS: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
14 3116711
14 3149603
13 3025997
12 3066946
14 3149997
15 3054420
12 2988663
12 3002010
11 3239410
9 2989776
9 3016848
9 3020691
9 3019183
9 3014441
9 3069934
9 3030128
9 3148442
9 3179266
8 3072189
9 3115689
9 3226327
8 2925988
8 3072690
8 2955707
8 3018875
8 2970570
8 2946374
8 3042341
8 3099590
8 3039751
8 2934592
8 2857685
8 2832950
7 2745440
7 2826198
6 2583010
7 2813985
6 2395557
6 2333217
6 2299194
FINISHED RECURSIVE SORTS: 0
SORTED NEW EDGES: 2
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 1
10 10485760
10 10485760
10 10485760
10 10485760
10 10485760
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
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9437184
9 9106051
FINISHED RECURSIVE SORTS: 1
RE-SORTED NODES: 4
PROCESS EDGES: 2
REMOVE Y: 0
COUNT NUMBER IN EACH BIN: 0
FINISHED FIRST ROUND: 0
10 10486331
10 10486749
10 10487477
10 10486402
10 10489112
9 9445222
9 9447928
9 9458342
9 9442282
9 9438310
9 9438279
9 9438230
9 9439494
9 9446330
9 9441876
9 9450943
9 9444619
9 9442529
9 9450324
9 9448467
9 9439955
9 9440618
9 9439941
9 9441096
9 9443618
9 9440517
9 9440032
9 9438447
9 9438976
9 9438118
9 9438335
9 9437708
9 9437808
9 9437871
9 9437892
9 9437999
9 9438119
9 9438441
9 9438110
9 9106866
FINISHED RECURSIVE SORTS: 1
SORT, Make index: 4
TOTAL: 17
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 118357755
fchr[G]: 191263101
fchr[T]: 264169327
fchr[$]: 382559712
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 240781428 bytes to primary GFM file: Pver_genome_assembly_v1.0.1.ht2
Wrote 95599784 bytes to secondary GFM file: Pver_genome_assembly_v1.0.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 396980515 bytes to primary GFM file: Pver_genome_assembly_v1.0.5.ht2
Wrote 96591138 bytes to secondary GFM file: Pver_genome_assembly_v1.0.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 379995663
    gbwtLen: 382559713
    nodes: 382399106
    sz: 189997832
    gbwtSz: 191279857
    lineRate: 7
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 23899945
    offsSz: 95599780
    lineSz: 128
    sideSz: 128
    sideGbwtSz: 104
    sideGbwtLen: 208
    numSides: 1839230
    numLines: 1839230
    gbwtTotLen: 235421440
    gbwtTotSz: 235421440
    reverse: 0
    linearFM: No
Total time for call to driver() for forward index: 00:08:09