Settings:
  Output files: "/projects/NBL/HS1197/311NGAAXX_5/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/HS1197/311NGAAXX_5/tophat_wj/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:19
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:14
bmax according to bmaxDivN setting: 55716952
Using parameters --bmax 41787714 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 41787714 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:09
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:02
  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: 00:00:18
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.18383e+07 (target: 41787713)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (41787714) 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 30179916
  (Using difference cover)
  Sorting block time: 00:00:30
Returning block of 30179917
Getting block 2 of 7
  Reserving size (41787714) 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 27588559
  (Using difference cover)
  Sorting block time: 00:00:29
Returning block of 27588560
Getting block 3 of 7
  Reserving size (41787714) 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 39526817
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 39526818
Getting block 4 of 7
  Reserving size (41787714) 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 34200158
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 34200159
Getting block 5 of 7
  Reserving size (41787714) 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 40889838
  (Using difference cover)
  Sorting block time: 00:00:46
Returning block of 40889839
Getting block 6 of 7
  Reserving size (41787714) 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 35674524
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 35674525
Getting block 7 of 7
  Reserving size (41787714) 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 14807992
  (Using difference cover)
  Sorting block time: 00:00:12
Returning block of 14807993
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 58405375
fchr[G]: 111981162
fchr[T]: 164401650
fchr[$]: 222867810
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 407725918 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_5/tophat_wj/tmp/segment_juncs.1.ebwt
Wrote 27858484 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_5/tophat_wj/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 222867810
    bwtLen: 222867811
    sz: 55716953
    bwtSz: 55716953
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 6964620
    offsSz: 27858480
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 497473
    numSides: 994946
    numLines: 994946
    ebwtTotLen: 63676544
    ebwtTotSz: 63676544
Total time for call to driver() for forward index: 00:06:28
Reading reference sizes
  Time reading reference sizes: 00:00:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:13
bmax according to bmaxDivN setting: 55716952
Using parameters --bmax 41787714 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 41787714 --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: 00:00:02
  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: 00:00:17
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: 00:00:14
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; 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: 00:00:13
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.18383e+07 (target: 41787713)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (41787714) 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 38203747
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 38203748
Getting block 2 of 7
  Reserving size (41787714) 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 27275281
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 27275282
Getting block 3 of 7
  Reserving size (41787714) 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 34494304
  (Using difference cover)
  Sorting block time: 00:00:41
Returning block of 34494305
Getting block 4 of 7
  Reserving size (41787714) 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 31913392
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 31913393
Getting block 5 of 7
  Reserving size (41787714) 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 35173386
  (Using difference cover)
  Sorting block time: 00:00:38
Returning block of 35173387
Getting block 6 of 7
  Reserving size (41787714) 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 20486163
  (Using difference cover)
  Sorting block time: 00:00:23
Returning block of 20486164
Getting block 7 of 7
  Reserving size (41787714) 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 35321531
  (Using difference cover)
  Sorting block time: 00:00:36
Returning block of 35321532
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 58405375
fchr[G]: 111981162
fchr[T]: 164401650
fchr[$]: 222867810
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 407725918 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_5/tophat_wj/tmp/segment_juncs.rev.1.ebwt
Wrote 27858484 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_5/tophat_wj/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 222867810
    bwtLen: 222867811
    sz: 55716953
    bwtSz: 55716953
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 6964620
    offsSz: 27858480
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 497473
    numSides: 994946
    numLines: 994946
    ebwtTotLen: 63676544
    ebwtTotSz: 63676544
Total time for backward call to driver() for mirror index: 00:06:54