Settings:
  Output files: "/projects/NBL/HS1803/616GYAAXX_5/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/HS1803/616GYAAXX_5/tophat/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:02:11
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:34
bmax according to bmaxDivN setting: 102075909
Using parameters --bmax 76556932 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76556932 --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: 00:00:10
  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: 00:00:48
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 5; iterating...
  Binary sorting into buckets
  10%
  20%
  30%
  40%
  50%
  60%
  70%
  80%
  90%
  100%
  Binary sorting into buckets time: 00:00:45
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 4.53671e+07 (target: 76556931)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 9
  Reserving size (76556932) 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 21896057
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 21896058
Getting block 2 of 9
  Reserving size (76556932) 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 68665793
  (Using difference cover)
  Sorting block time: 00:01:39
Returning block of 68665794
Getting block 3 of 9
  Reserving size (76556932) 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 16491890
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 16491891
Getting block 4 of 9
  Reserving size (76556932) 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 62270001
  (Using difference cover)
  Sorting block time: 00:01:37
Returning block of 62270002
Getting block 5 of 9
  Reserving size (76556932) 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: 00:00:18
  Sorting block of length 20437715
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 20437716
Getting block 6 of 9
  Reserving size (76556932) 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: 00:00:19
  Sorting block of length 67293620
  (Using difference cover)
  Sorting block time: 00:01:43
Returning block of 67293621
Getting block 7 of 9
  Reserving size (76556932) 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: 00:00:19
  Sorting block of length 42453755
  (Using difference cover)
  Sorting block time: 00:01:05
Returning block of 42453756
Getting block 8 of 9
  Reserving size (76556932) 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: 00:00:21
  Sorting block of length 70471200
  (Using difference cover)
  Sorting block time: 00:01:42
Returning block of 70471201
Getting block 9 of 9
  Reserving size (76556932) 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 38323599
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 38323600
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104568863
fchr[G]: 202975582
fchr[T]: 300320010
fchr[$]: 408303638
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 741763281 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_5/tophat/tmp/segment_juncs.1.ebwt
Wrote 51037960 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_5/tophat/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 408303638
    bwtLen: 408303639
    sz: 102075910
    bwtSz: 102075910
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12759489
    offsSz: 51037956
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 911393
    numSides: 1822786
    numLines: 1822786
    ebwtTotLen: 116658304
    ebwtTotSz: 116658304
Total time for call to driver() for forward index: 00:20:12
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: 00:00:33
bmax according to bmaxDivN setting: 102075909
Using parameters --bmax 76556932 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 76556932 --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: 00:00:12
  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: 00:00:46
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: 00:00:41
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 5.83291e+07 (target: 76556931)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (76556932) 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 57333485
  (Using difference cover)
  Sorting block time: 00:01:18
Returning block of 57333486
Getting block 2 of 7
  Reserving size (76556932) 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 37390604
  (Using difference cover)
  Sorting block time: 00:00:53
Returning block of 37390605
Getting block 3 of 7
  Reserving size (76556932) 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 41430211
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 41430212
Getting block 4 of 7
  Reserving size (76556932) 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: 00:00:18
  Sorting block of length 70491309
  (Using difference cover)
  Sorting block time: 00:01:51
Returning block of 70491310
Getting block 5 of 7
  Reserving size (76556932) 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: 00:00:19
  Sorting block of length 56908312
  (Using difference cover)
  Sorting block time: 00:01:31
Returning block of 56908313
Getting block 6 of 7
  Reserving size (76556932) 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: 00:00:21
  Sorting block of length 73995012
  (Using difference cover)
  Sorting block time: 00:01:47
Returning block of 73995013
Getting block 7 of 7
  Reserving size (76556932) 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 70754699
  (Using difference cover)
  Sorting block time: 00:01:40
Returning block of 70754700
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 104568863
fchr[G]: 202975582
fchr[T]: 300320010
fchr[$]: 408303638
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 741763281 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_5/tophat/tmp/segment_juncs.rev.1.ebwt
Wrote 51037960 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_5/tophat/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 408303638
    bwtLen: 408303639
    sz: 102075910
    bwtSz: 102075910
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 12759489
    offsSz: 51037956
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 911393
    numSides: 1822786
    numLines: 1822786
    ebwtTotLen: 116658304
    ebwtTotSz: 116658304
Total time for backward call to driver() for mirror index: 00:17:34