[seanb80@n2193 BGI_Big_Assembly]$ /gscratch/srlab/programs/bowtie2-2.1.0/bowtie2-build BGI_Oly_Scaffolds.fa BGI_Oly_Big
Settings:
  Output files: "BGI_Oly_Big.*.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:
  BGI_Oly_Scaffolds.fa
Reading reference sizes
  Time reading reference sizes: 00:00:18
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:17
bmax according to bmaxDivN setting: 548603233
Using parameters --bmax 411452425 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 411452425 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:34
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:09
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:18
  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
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  Binary sorting into buckets time: 00:01:12
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:01:04
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.74302e+08 (target: 411452424)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:19
  Sorting block of length 159354977
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 159354978
Getting block 2 of 8
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:25
  Sorting block of length 408373758
  (Using difference cover)
  Sorting block time: 00:01:40
Returning block of 408373759
Getting block 3 of 8
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:28
  Sorting block of length 211379897
  (Using difference cover)
  Sorting block time: 00:00:50
Returning block of 211379898
Getting block 4 of 8
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:29
  Sorting block of length 278794435
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 278794436
Getting block 5 of 8
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:33
  Sorting block of length 358439309
  (Using difference cover)
  Sorting block time: 00:01:25
Returning block of 358439310
Getting block 6 of 8
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:31
  Sorting block of length 216315998
  (Using difference cover)
  Sorting block time: 00:00:51
Returning block of 216315999
Getting block 7 of 8
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:29
  Sorting block of length 400058176
  (Using difference cover)
  Sorting block time: 00:01:37
Returning block of 400058177
Getting block 8 of 8
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:20
  Sorting block of length 161696375
  (Using difference cover)
  Sorting block time: 00:00:37
Returning block of 161696376
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 688151346
fchr[G]: 1100657003
fchr[T]: 1510447924
fchr[$]: 2194412932
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 1154511776 bytes to primary EBWT file: BGI_Oly_Big.1.bt2
Wrote 548603240 bytes to secondary EBWT file: BGI_Oly_Big.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2194412932
    bwtLen: 2194412933
    sz: 548603233
    bwtSz: 548603234
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 137150809
    offsSz: 548603236
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 11429235
    numLines: 11429235
    ebwtTotLen: 731471040
    ebwtTotSz: 731471040
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:18:51
Reading reference sizes
  Time reading reference sizes: 00:00:13
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:17
  Time to reverse reference sequence: 00:00:03
bmax according to bmaxDivN setting: 548603233
Using parameters --bmax 411452425 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 411452425 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:34
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:09
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:18
  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
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  Binary sorting into buckets time: 00:01:14
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:01:04
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:01:03
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
  Binary sorting into buckets
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  Binary sorting into buckets time: 00:01:03
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3.13488e+08 (target: 411452424)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 268533187
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 268533188
Getting block 2 of 7
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:25
  Sorting block of length 405570344
  (Using difference cover)
  Sorting block time: 00:01:39
Returning block of 405570345
Getting block 3 of 7
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:29
  Sorting block of length 362061828
  (Using difference cover)
  Sorting block time: 00:01:27
Returning block of 362061829
Getting block 4 of 7
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:33
  Sorting block of length 403151400
  (Using difference cover)
  Sorting block time: 00:01:36
Returning block of 403151401
Getting block 5 of 7
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:32
  Sorting block of length 330105464
  (Using difference cover)
  Sorting block time: 00:01:19
Returning block of 330105465
Getting block 6 of 7
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:29
  Sorting block of length 170787128
  (Using difference cover)
  Sorting block time: 00:00:39
Returning block of 170787129
Getting block 7 of 7
  Reserving size (411452425) for bucket
  Calculating Z arrays
  Calculating Z arrays time: 00:00:00
  Entering block accumulator loop:
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  Block accumulator loop time: 00:00:21
  Sorting block of length 254203575
  (Using difference cover)
  Sorting block time: 00:00:59
Returning block of 254203576
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 688151346
fchr[G]: 1100657003
fchr[T]: 1510447924
fchr[$]: 2194412932
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 1154511776 bytes to primary EBWT file: BGI_Oly_Big.rev.1.bt2
Wrote 548603240 bytes to secondary EBWT file: BGI_Oly_Big.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 2194412932
    bwtLen: 2194412933
    sz: 548603233
    bwtSz: 548603234
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 137150809
    offsSz: 548603236
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 11429235
    numLines: 11429235
    ebwtTotLen: 731471040
    ebwtTotSz: 731471040
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:20:33
[seanb80@n2193 BGI_Big_Assembly]$ cd ..