Settings:
  Output files: "/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W3_08594/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:
  /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W3_08594/tmp/segment_juncs.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 2822387
Using parameters --bmax 2116791 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 2116791 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  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: 00:00:01
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: 00:00:00
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: 00:00:00
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: 00:00:01
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: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.41119e+06 (target: 2116790)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1459517
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1459518
Getting block 2 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1893504
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1893505
Getting block 3 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 511499
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 511500
Getting block 4 of 8
  Reserving size (2116791) 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: 00:00:01
  Sorting block of length 1680271
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1680272
Getting block 5 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1437721
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1437722
Getting block 6 of 8
  Reserving size (2116791) 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: 00:00:01
  Sorting block of length 1750983
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1750984
Getting block 7 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 547707
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 547708
Getting block 8 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 2008341
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 2008342
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2800857
fchr[G]: 5640264
fchr[T]: 8482765
fchr[$]: 11289550
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 22657326 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W3_08594/tmp/segment_juncs.1.ebwt
Wrote 1411200 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W3_08594/tmp/segment_juncs.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 11289550
    bwtLen: 11289551
    sz: 2822388
    bwtSz: 2822388
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 352799
    offsSz: 1411196
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 25200
    numSides: 50400
    numLines: 50400
    ebwtTotLen: 3225600
    ebwtTotSz: 3225600
    reverse: 0
Total time for call to driver() for forward index: 00:00:06
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 2822387
Using parameters --bmax 2116791 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 2116791 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:01
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  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: 00:00:00
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 1.41119e+06 (target: 2116790)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1855809
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1855810
Getting block 2 of 8
  Reserving size (2116791) 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: 00:00:01
  Sorting block of length 1276721
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1276722
Getting block 3 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1067886
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1067887
Getting block 4 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1759382
  (Using difference cover)
  Sorting block time: 00:00:01
Returning block of 1759383
Getting block 5 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1135414
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1135415
Getting block 6 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1278600
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1278601
Getting block 7 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1565194
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1565195
Getting block 8 of 8
  Reserving size (2116791) 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: 00:00:00
  Sorting block of length 1350537
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 1350538
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 2800857
fchr[G]: 5640264
fchr[T]: 8482765
fchr[$]: 11289550
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 22657326 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W3_08594/tmp/segment_juncs.rev.1.ebwt
Wrote 1411200 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W3_08594/tmp/segment_juncs.rev.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 11289550
    bwtLen: 11289551
    sz: 2822388
    bwtSz: 2822388
    lineRate: 6
    linesPerSide: 1
    offRate: 5
    offMask: 0xffffffe0
    isaRate: -1
    isaMask: 0xffffffff
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 352799
    offsSz: 1411196
    isaLen: 0
    isaSz: 0
    lineSz: 64
    sideSz: 64
    sideBwtSz: 56
    sideBwtLen: 224
    numSidePairs: 25200
    numSides: 50400
    numLines: 50400
    ebwtTotLen: 3225600
    ebwtTotSz: 3225600
    reverse: 0
Total time for backward call to driver() for mirror index: 00:00:05