Settings:
  Output files: "/projects/NBL/HS1196/3153YAAXX_7/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_7/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:14
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:09
bmax according to bmaxDivN setting: 39756085
Using parameters --bmax 29817064 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 29817064 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:06
  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: 00:00:13
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: 00:00:12
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: 00:00:13
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: 00:00:12
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: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.9878e+07 (target: 29817063)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (29817064) 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 23437591
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 23437592
Getting block 2 of 8
  Reserving size (29817064) 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 16991153
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 16991154
Getting block 3 of 8
  Reserving size (29817064) 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 15273851
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 15273852
Getting block 4 of 8
  Reserving size (29817064) 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 22341898
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 22341899
Getting block 5 of 8
  Reserving size (29817064) 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 14608867
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 14608868
Getting block 6 of 8
  Reserving size (29817064) 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 25974645
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 25974646
Getting block 7 of 8
  Reserving size (29817064) 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 16504214
  (Using difference cover)
  Sorting block time: 00:00:19
Returning block of 16504215
Getting block 8 of 8
  Reserving size (29817064) 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 23892114
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 23892115
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 40428746
fchr[G]: 79702926
fchr[T]: 118317659
fchr[$]: 159024340
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 291393414 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_7/tophat/tmp/segment_juncs.1.ebwt
Wrote 19878048 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_7/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 159024340
    bwtLen: 159024341
    sz: 39756085
    bwtSz: 39756086
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4969511
    offsSz: 19878044
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 354966
    numSides: 709932
    numLines: 709932
    ebwtTotLen: 45435648
    ebwtTotSz: 45435648
Total time for call to driver() for forward index: 00:05:49
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: 00:00:09
bmax according to bmaxDivN setting: 39756085
Using parameters --bmax 29817064 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 29817064 --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: 00:00:02
  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: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.27178e+07 (target: 29817063)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (29817064) 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 12956926
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 12956927
Getting block 2 of 7
  Reserving size (29817064) 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 24387689
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 24387690
Getting block 3 of 7
  Reserving size (29817064) 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 19782147
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 19782148
Getting block 4 of 7
  Reserving size (29817064) 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 28389958
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 28389959
Getting block 5 of 7
  Reserving size (29817064) 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 27928082
  (Using difference cover)
  Sorting block time: 00:00:44
Returning block of 27928083
Getting block 6 of 7
  Reserving size (29817064) 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 18348747
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 18348748
Getting block 7 of 7
  Reserving size (29817064) 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 27230785
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 27230786
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 40428746
fchr[G]: 79702926
fchr[T]: 118317659
fchr[$]: 159024340
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 291393414 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_7/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 19878048 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_7/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 159024340
    bwtLen: 159024341
    sz: 39756085
    bwtSz: 39756086
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 4969511
    offsSz: 19878044
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 354966
    numSides: 709932
    numLines: 709932
    ebwtTotLen: 45435648
    ebwtTotSz: 45435648
Total time for backward call to driver() for mirror index: 00:05:42