Settings:
  Output files: "/projects/NBL/HS1801/61074AAXX_6/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/HS1801/61074AAXX_6/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:01:37
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:24
bmax according to bmaxDivN setting: 101637023
Using parameters --bmax 76227768 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76227768 --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: 00:00:04
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:07
  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: 00:00:30
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 8; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:22
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:22
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 0; 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
Split 1, merged 1; 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
Split 1, merged 1; iterating...
Avg bucket size: 5.08185e+07 (target: 76227767)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (76227768) 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 54790989
  (Using difference cover)
  Sorting block time: 00:00:43
Returning block of 54790990
Getting block 2 of 8
  Reserving size (76227768) 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 73321221
  (Using difference cover)
  Sorting block time: 00:01:03
Returning block of 73321222
Getting block 3 of 8
  Reserving size (76227768) 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 73572877
  (Using difference cover)
  Sorting block time: 00:01:08
Returning block of 73572878
Getting block 4 of 8
  Reserving size (76227768) 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 11170422
  (Using difference cover)
  Sorting block time: 00:00:09
Returning block of 11170423
Getting block 5 of 8
  Reserving size (76227768) 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 21264318
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 21264319
Getting block 6 of 8
  Reserving size (76227768) 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 73975973
  (Using difference cover)
  Sorting block time: 00:01:07
Returning block of 73975974
Getting block 7 of 8
  Reserving size (76227768) 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 24375594
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 24375595
Getting block 8 of 8
  Reserving size (76227768) 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 74076691
  (Using difference cover)
  Sorting block time: 00:01:03
Returning block of 74076692
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101115360
fchr[G]: 201685090
fchr[T]: 302117803
fchr[$]: 406548092
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 738198519 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_6/tophat/tmp/segment_juncs.1.ebwt
Wrote 50818516 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_6/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 406548092
    bwtLen: 406548093
    sz: 101637023
    bwtSz: 101637024
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12704628
    offsSz: 50818512
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 907474
    numSides: 1814948
    numLines: 1814948
    ebwtTotLen: 116156672
    ebwtTotSz: 116156672
Total time for call to driver() for forward index: 00:13:35
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: 00:00:26
bmax according to bmaxDivN setting: 101637023
Using parameters --bmax 76227768 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76227768 --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: 00:00:07
  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
Split 1, merged 7; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:23
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.80783e+07 (target: 76227767)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76227768) 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 64488747
  (Using difference cover)
  Sorting block time: 00:00:54
Returning block of 64488748
Getting block 2 of 7
  Reserving size (76227768) 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 59259042
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 59259043
Getting block 3 of 7
  Reserving size (76227768) 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 49163107
  (Using difference cover)
  Sorting block time: 00:00:47
Returning block of 49163108
Getting block 4 of 7
  Reserving size (76227768) 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 28774190
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 28774191
Getting block 5 of 7
  Reserving size (76227768) 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 64505303
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 64505304
Getting block 6 of 7
  Reserving size (76227768) 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 69669942
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 69669943
Getting block 7 of 7
  Reserving size (76227768) 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 70687755
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 70687756
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 101115360
fchr[G]: 201685090
fchr[T]: 302117803
fchr[$]: 406548092
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 738198519 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_6/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 50818516 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_6/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 406548092
    bwtLen: 406548093
    sz: 101637023
    bwtSz: 101637024
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12704628
    offsSz: 50818512
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 907474
    numSides: 1814948
    numLines: 1814948
    ebwtTotLen: 116156672
    ebwtTotSz: 116156672
Total time for backward call to driver() for mirror index: 00:10:23