Writing bisulfite genomes out into a single MFA (multi FastA) file

Bisulfite Genome Indexer version v0.16.0 (last modified 25 August 2015)


Step I - Prepare genome folders - completed



Total number of conversions performed:
C->T:	34912524
G->A:	35019119

Step II - Genome bisulfite conversions - completed


Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer
Please be aware that this process can - depending on genome size - take several hours!
Settings:
  Output files: "BS_CT.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  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:
  genome_mfa.CT_conversion.fa
Building a SMALL index
Reading reference sizes
Settings:
  Output files: "BS_GA.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  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:
  genome_mfa.GA_conversion.fa
Building a SMALL index
Reading reference sizes
  Time reading reference sizes: 00:00:04
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time reading reference sizes: 00:00:04
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:02
bmax according to bmaxDivN setting: 44188531
Using parameters --bmax 33141399 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 33141399 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  Time to join reference sequences: 00:00:03
bmax according to bmaxDivN setting: 44188531
Using parameters --bmax 33141399 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 33141399 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:05
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:02
  Invoking Larsson-Sadakane on ranks
  V-Sorting samples time: 00:00:07
  Allocating rank array
  Ranking v-sort output
  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
  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
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.20943e+07 (target: 33141398)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (33141399) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 12238483 for bucket 1
  (Using difference cover)
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.20943e+07 (target: 33141398)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (33141399) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  Sorting block time: 00:00:08
Returning block of 12238484 for bucket 1
  bucket 1: 100%
  Sorting block of length 13510303 for bucket 1
  (Using difference cover)
Getting block 2 of 8
  Reserving size (33141399) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 26072116 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:11
Returning block of 13510304 for bucket 1
Getting block 2 of 8
  Reserving size (33141399) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 28828516 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 26072117 for bucket 2
Getting block 3 of 8
  Reserving size (33141399) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 15821008 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:25
Returning block of 28828517 for bucket 2
  Sorting block time: 00:00:13
Returning block of 15821009 for bucket 3
Getting block 3 of 8
  Reserving size (33141399) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
Getting block 4 of 8
  Reserving size (33141399) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 3: 30%
  bucket 4: 10%
  bucket 3: 40%
  bucket 4: 20%
  bucket 3: 50%
  bucket 4: 30%
  bucket 3: 60%
  bucket 4: 40%
  bucket 3: 70%
  bucket 4: 50%
  bucket 3: 80%
  bucket 4: 60%
  bucket 3: 90%
  bucket 4: 70%
  bucket 3: 100%
  Sorting block of length 26448887 for bucket 3
  (Using difference cover)
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 31494517 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 26448888 for bucket 3
  Sorting block time: 00:00:26
Returning block of 31494518 for bucket 4
Getting block 4 of 8
  Reserving size (33141399) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 18431349 for bucket 4
  (Using difference cover)
Getting block 5 of 8
  Reserving size (33141399) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 24587755 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:16
Returning block of 18431350 for bucket 4
Getting block 5 of 8
  Reserving size (33141399) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  Sorting block time: 00:00:20
Returning block of 24587756 for bucket 5
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 21429650 for bucket 5
  (Using difference cover)
Getting block 6 of 8
  Reserving size (33141399) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 27130046 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:21
Returning block of 21429651 for bucket 5
Getting block 6 of 8
  Reserving size (33141399) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 32967759 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 27130047 for bucket 6
Getting block 7 of 8
  Reserving size (33141399) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 20765011 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:18
Returning block of 20765012 for bucket 7
Getting block 8 of 8
  Reserving size (33141399) for bucket 8
  Calculating Z arrays for bucket 8
  Entering block accumulator loop for bucket 8:
  Sorting block time: 00:00:34
Returning block of 32967760 for bucket 6
  bucket 8: 10%
  bucket 8: 20%
  bucket 8: 30%
  bucket 8: 40%
  bucket 8: 50%
  bucket 8: 60%
  bucket 8: 70%
  bucket 8: 80%
  bucket 8: 90%
  bucket 8: 100%
  Sorting block of length 18645183 for bucket 8
  (Using difference cover)
Getting block 7 of 8
  Reserving size (33141399) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 27419503 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:15
Returning block of 18645184 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 53316577
fchr[G]: 53316577
fchr[T]: 88335696
fchr[$]: 176754126
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 63113041 bytes to primary EBWT file: BS_CT.1.bt2
Wrote 44188536 bytes to secondary EBWT file: BS_CT.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 176754126
    bwtLen: 176754127
    sz: 44188532
    bwtSz: 44188532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11047133
    offsSz: 44188532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 920595
    numLines: 920595
    ebwtTotLen: 58918080
    ebwtTotSz: 58918080
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:03:59
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: 00:00:02
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 44188531
Using parameters --bmax 33141399 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 33141399 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:05
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:01
  Invoking Larsson-Sadakane on ranks
  Sorting block time: 00:00:21
Returning block of 27419504 for bucket 7
  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
Getting block 8 of 8
  Reserving size (33141399) for bucket 8
  Calculating Z arrays for bucket 8
  Entering block accumulator loop for bucket 8:
  bucket 8: 10%
  bucket 8: 20%
  bucket 8: 30%
  bucket 8: 40%
  bucket 8: 50%
  bucket 8: 60%
  bucket 8: 70%
  bucket 8: 80%
  bucket 8: 90%
  bucket 8: 100%
  Sorting block of length 7718152 for bucket 8
  (Using difference cover)
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  Sorting block time: 00:00:06
Returning block of 7718153 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 88335696
fchr[G]: 123248220
fchr[T]: 123248220
fchr[$]: 176754126
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 63113041 bytes to primary EBWT file: BS_GA.1.bt2
Wrote 44188536 bytes to secondary EBWT file: BS_GA.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 176754126
    bwtLen: 176754127
    sz: 44188532
    bwtSz: 44188532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11047133
    offsSz: 44188532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 920595
    numLines: 920595
    ebwtTotLen: 58918080
    ebwtTotSz: 58918080
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:04:26
Reading reference sizes
  Time reading reference sizes: 00:00:02
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.52506e+07 (target: 33141398)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (33141399) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  Time to join reference sequences: 00:00:03
  Time to reverse reference sequence: 00:00:01
bmax according to bmaxDivN setting: 44188531
Using parameters --bmax 33141399 --dcv 1024
  Doing ahead-of-time memory usage test
  bucket 1: 60%
  Passed!  Constructing with these parameters: --bmax 33141399 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  bucket 1: 70%
  Building sPrimeOrder
  V-Sorting samples
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 20557813 for bucket 1
  (Using difference cover)
  V-Sorting samples time: 00:00:07
  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: 00:00:02
  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
  Sorting block time: 00:00:12
Returning block of 20557814 for bucket 1
Getting block 2 of 7
  Reserving size (33141399) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 30464357 for bucket 2
  (Using difference cover)
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Sorting block time: 00:00:19
Returning block of 30464358 for bucket 2
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.52506e+07 (target: 33141398)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (33141399) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
Getting block 3 of 7
  Reserving size (33141399) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 1: 90%
  bucket 3: 10%
  bucket 1: 100%
  Sorting block of length 25807013 for bucket 1
  (Using difference cover)
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 10560539 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:07
Returning block of 10560540 for bucket 3
Getting block 4 of 7
  Reserving size (33141399) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 28834729 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 25807014 for bucket 1
Getting block 2 of 7
  Reserving size (33141399) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 25872094 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:20
Returning block of 28834730 for bucket 4
Getting block 5 of 7
  Reserving size (33141399) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 32883003 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:26
Returning block of 25872095 for bucket 2
Getting block 3 of 7
  Reserving size (33141399) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 26343422 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:22
Returning block of 32883004 for bucket 5
Getting block 6 of 7
  Reserving size (33141399) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 28411430 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:28
Returning block of 26343423 for bucket 3
  Sorting block time: 00:00:19
Returning block of 28411431 for bucket 6
Getting block 7 of 7
  Reserving size (33141399) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
Getting block 4 of 7
  Reserving size (33141399) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 7: 10%
  bucket 4: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 4: 20%
  bucket 7: 40%
  bucket 7: 50%
  bucket 4: 30%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 4: 40%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 25042249 for bucket 7
  (Using difference cover)
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 26137893 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:17
Returning block of 25042250 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 53316577
fchr[G]: 53316577
fchr[T]: 88335696
fchr[$]: 176754126
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 63113041 bytes to primary EBWT file: BS_CT.rev.1.bt2
Wrote 44188536 bytes to secondary EBWT file: BS_CT.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 176754126
    bwtLen: 176754127
    sz: 44188532
    bwtSz: 44188532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11047133
    offsSz: 44188532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 920595
    numLines: 920595
    ebwtTotLen: 58918080
    ebwtTotSz: 58918080
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:03:28
  Sorting block time: 00:00:28
Returning block of 26137894 for bucket 4
Getting block 5 of 7
  Reserving size (33141399) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 31003341 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:32
Returning block of 31003342 for bucket 5
Getting block 6 of 7
  Reserving size (33141399) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 27779187 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:31
Returning block of 27779188 for bucket 6
Getting block 7 of 7
  Reserving size (33141399) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 13811170 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:14
Returning block of 13811171 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 88335696
fchr[G]: 123248220
fchr[T]: 123248220
fchr[$]: 176754126
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 63113041 bytes to primary EBWT file: BS_GA.rev.1.bt2
Wrote 44188536 bytes to secondary EBWT file: BS_GA.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 176754126
    bwtLen: 176754127
    sz: 44188532
    bwtSz: 44188532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 11047133
    offsSz: 44188532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 920595
    numLines: 920595
    ebwtTotLen: 58918080
    ebwtTotSz: 58918080
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:05:04