Settings:
  Output files: "/projects/NBL/HS1795/700B4AAXX_2/tophat_wj/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/HS1795/700B4AAXX_2/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:52
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:26
bmax according to bmaxDivN setting: 102788858
Using parameters --bmax 77091644 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77091644 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:15
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:03
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:08
  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: 00:00:34
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: 00:00:25
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.13944e+07 (target: 77091643)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (77091644) 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 46390983
  (Using difference cover)
  Sorting block time: 00:00:35
Returning block of 46390984
Getting block 2 of 8
  Reserving size (77091644) 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: 00:00:10
  Sorting block of length 67908058
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 67908059
Getting block 3 of 8
  Reserving size (77091644) 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: 00:00:11
  Sorting block of length 50909982
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 50909983
Getting block 4 of 8
  Reserving size (77091644) 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 56863595
  (Using difference cover)
  Sorting block time: 00:00:47
Returning block of 56863596
Getting block 5 of 8
  Reserving size (77091644) 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 58783263
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 58783264
Getting block 6 of 8
  Reserving size (77091644) 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 39690262
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 39690263
Getting block 7 of 8
  Reserving size (77091644) 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 70732450
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 70732451
Getting block 8 of 8
  Reserving size (77091644) 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 19876832
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 19876833
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102964806
fchr[G]: 203748714
fchr[T]: 304529169
fchr[$]: 411155432
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 747158125 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_2/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 51394436 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_2/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 411155432
    bwtLen: 411155433
    sz: 102788858
    bwtSz: 102788859
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12848608
    offsSz: 51394432
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 917758
    numSides: 1835516
    numLines: 1835516
    ebwtTotLen: 117473024
    ebwtTotSz: 117473024
Total time for call to driver() for forward index: 00:11:02
Reading reference sizes
  Time reading reference sizes: 00:00:07
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:25
bmax according to bmaxDivN setting: 102788858
Using parameters --bmax 77091644 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 77091644 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:15
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:03
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:06
  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: 00:00:37
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.87365e+07 (target: 77091643)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (77091644) 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 46719383
  (Using difference cover)
  Sorting block time: 00:00:34
Returning block of 46719384
Getting block 2 of 7
  Reserving size (77091644) 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 75967093
  (Using difference cover)
  Sorting block time: 00:01:01
Returning block of 75967094
Getting block 3 of 7
  Reserving size (77091644) 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 63047144
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 63047145
Getting block 4 of 7
  Reserving size (77091644) 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 52651004
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 52651005
Getting block 5 of 7
  Reserving size (77091644) 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 61747543
  (Using difference cover)
  Sorting block time: 00:00:52
Returning block of 61747544
Getting block 6 of 7
  Reserving size (77091644) 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 37866391
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 37866392
Getting block 7 of 7
  Reserving size (77091644) 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 73156868
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 73156869
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 102964806
fchr[G]: 203748714
fchr[T]: 304529169
fchr[$]: 411155432
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 747158125 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_2/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 51394436 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_2/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 411155432
    bwtLen: 411155433
    sz: 102788858
    bwtSz: 102788859
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12848608
    offsSz: 51394432
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 917758
    numSides: 1835516
    numLines: 1835516
    ebwtTotLen: 117473024
    ebwtTotSz: 117473024
Total time for backward call to driver() for mirror index: 00:09:36