Settings:
  Output files: "/projects/NBL/HS1195/30TTYAAXX_2/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/HS1195/30TTYAAXX_2/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:08
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:23
bmax according to bmaxDivN setting: 91928447
Using parameters --bmax 68946336 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 68946336 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:29
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:05
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:11
  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: 00:00:33
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.08571e+07 (target: 68946335)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 9
  Reserving size (68946336) 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: 00:00:09
  Sorting block of length 18648924
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 18648925
Getting block 2 of 9
  Reserving size (68946336) 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: 00:00:12
  Sorting block of length 52816985
  (Using difference cover)
  Sorting block time: 00:01:33
Returning block of 52816986
Getting block 3 of 9
  Reserving size (68946336) 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: 00:00:12
  Sorting block of length 38075834
  (Using difference cover)
  Sorting block time: 00:01:08
Returning block of 38075835
Getting block 4 of 9
  Reserving size (68946336) 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: 00:00:12
  Sorting block of length 44562600
  (Using difference cover)
  Sorting block time: 00:01:31
Returning block of 44562601
Getting block 5 of 9
  Reserving size (68946336) 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: 00:00:14
  Sorting block of length 56386422
  (Using difference cover)
  Sorting block time: 00:01:55
Returning block of 56386423
Getting block 6 of 9
  Reserving size (68946336) 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: 00:00:14
  Sorting block of length 18175586
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 18175587
Getting block 7 of 9
  Reserving size (68946336) 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: 00:00:17
  Sorting block of length 60206986
  (Using difference cover)
  Sorting block time: 00:02:00
Returning block of 60206987
Getting block 8 of 9
  Reserving size (68946336) 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: 00:00:15
  Sorting block of length 44478428
  (Using difference cover)
  Sorting block time: 00:01:29
Returning block of 44478429
Getting block 9 of 9
  Reserving size (68946336) 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: 00:00:09
  Sorting block of length 34362016
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 34362017
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104739952
fchr[G]: 183167974
fchr[T]: 261311466
fchr[$]: 367713789
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 668614006 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_2/tophat/tmp/segment_juncs.1.ebwt
Wrote 45964228 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_2/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 367713789
    bwtLen: 367713790
    sz: 91928448
    bwtSz: 91928448
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11491056
    offsSz: 45964224
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 820790
    numSides: 1641580
    numLines: 1641580
    ebwtTotLen: 105061120
    ebwtTotSz: 105061120
Total time for call to driver() for forward index: 00:18:04
Reading reference sizes
  Time reading reference sizes: 00:00:08
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:23
bmax according to bmaxDivN setting: 91928447
Using parameters --bmax 68946336 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 68946336 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:30
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:06
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:10
  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: 00:00:32
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 5; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:37
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.08571e+07 (target: 68946335)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 9
  Reserving size (68946336) 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: 00:00:09
  Sorting block of length 44619143
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 44619144
Getting block 2 of 9
  Reserving size (68946336) 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: 00:00:12
  Sorting block of length 58175299
  (Using difference cover)
  Sorting block time: 00:01:55
Returning block of 58175300
Getting block 3 of 9
  Reserving size (68946336) 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: 00:00:13
  Sorting block of length 39507764
  (Using difference cover)
  Sorting block time: 00:01:19
Returning block of 39507765
Getting block 4 of 9
  Reserving size (68946336) 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: 00:00:13
  Sorting block of length 30135222
  (Using difference cover)
  Sorting block time: 00:01:03
Returning block of 30135223
Getting block 5 of 9
  Reserving size (68946336) 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: 00:00:16
  Sorting block of length 47302867
  (Using difference cover)
  Sorting block time: 00:01:37
Returning block of 47302868
Getting block 6 of 9
  Reserving size (68946336) 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: 00:00:15
  Sorting block of length 62206162
  (Using difference cover)
  Sorting block time: 00:02:06
Returning block of 62206163
Getting block 7 of 9
  Reserving size (68946336) 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: 00:00:15
  Sorting block of length 7826952
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 7826953
Getting block 8 of 9
  Reserving size (68946336) 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: 00:00:17
  Sorting block of length 64533124
  (Using difference cover)
  Sorting block time: 00:02:03
Returning block of 64533125
Getting block 9 of 9
  Reserving size (68946336) 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: 00:00:08
  Sorting block of length 13407248
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 13407249
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104739952
fchr[G]: 183167974
fchr[T]: 261311466
fchr[$]: 367713789
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 668614006 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_2/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 45964228 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_2/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 367713789
    bwtLen: 367713790
    sz: 91928448
    bwtSz: 91928448
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11491056
    offsSz: 45964224
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 820790
    numSides: 1641580
    numLines: 1641580
    ebwtTotLen: 105061120
    ebwtTotSz: 105061120
Total time for backward call to driver() for mirror index: 00:18:00