Settings:
  Output files: "/projects/NBL/HS1196/3153YAAXX_3/tophat/tmp/segment_juncs.*.ebwt"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 5 (one in 32)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 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:
  /projects/NBL/HS1196/3153YAAXX_3/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:13
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:10
bmax according to bmaxDivN setting: 39530920
Using parameters --bmax 29648190 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 29648190 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:07
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:12
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:10
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.25891e+07 (target: 29648189)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:03
  Sorting block of length 27352598
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 27352599
Getting block 2 of 7
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:04
  Sorting block of length 26379834
  (Using difference cover)
  Sorting block time: 00:00:33
Returning block of 26379835
Getting block 3 of 7
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:04
  Sorting block of length 20175759
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 20175760
Getting block 4 of 7
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:07
  Sorting block of length 21825461
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 21825462
Getting block 5 of 7
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:07
  Sorting block of length 29059758
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 29059759
Getting block 6 of 7
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:06
  Sorting block of length 16933710
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 16933711
Getting block 7 of 7
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:04
  Sorting block of length 16396554
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 16396555
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 40138983
fchr[G]: 79793145
fchr[T]: 117957047
fchr[$]: 158123680
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 289579089 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_3/tophat/tmp/segment_juncs.1.ebwt
Wrote 19765468 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_3/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 158123680
    bwtLen: 158123681
    sz: 39530920
    bwtSz: 39530921
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4941366
    offsSz: 19765464
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 352955
    numSides: 705910
    numLines: 705910
    ebwtTotLen: 45178240
    ebwtTotSz: 45178240
Total time for call to driver() for forward index: 00:05:37
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: 00:00:10
bmax according to bmaxDivN setting: 39530920
Using parameters --bmax 29648190 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 29648190 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:08
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:03
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:16
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:11
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.97655e+07 (target: 29648189)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:04
  Sorting block of length 24142669
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 24142670
Getting block 2 of 8
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:05
  Sorting block of length 16709220
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 16709221
Getting block 3 of 8
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:05
  Sorting block of length 24809448
  (Using difference cover)
  Sorting block time: 00:00:42
Returning block of 24809449
Getting block 4 of 8
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:05
  Sorting block of length 7416272
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 7416273
Getting block 5 of 8
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:07
  Sorting block of length 22569623
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 22569624
Getting block 6 of 8
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:05
  Sorting block of length 24712453
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 24712454
Getting block 7 of 8
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:06
  Sorting block of length 23228200
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 23228201
Getting block 8 of 8
  Reserving size (29648190) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Block accumulator loop time: 00:00:03
  Sorting block of length 14535788
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 14535789
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 40138983
fchr[G]: 79793145
fchr[T]: 117957047
fchr[$]: 158123680
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 289579089 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_3/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 19765468 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_3/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 158123680
    bwtLen: 158123681
    sz: 39530920
    bwtSz: 39530921
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4941366
    offsSz: 19765464
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 352955
    numSides: 705910
    numLines: 705910
    ebwtTotLen: 45178240
    ebwtTotSz: 45178240
Total time for backward call to driver() for mirror index: 00:05:29