Settings:
Output files: "/project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt.*.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:
/project2/NextGenMapTest/Teaser/references/GRCh37.fa
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:00:41
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:27
bmax according to bmaxDivN setting: 724327615
Using parameters --bmax 543245712 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 543245712 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:57
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:11
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:30
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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100%
Binary sorting into buckets time: 00:01:45
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Binary sorting into buckets
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100%
Binary sorting into buckets time: 00:01:28
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Binary sorting into buckets
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60%
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90%
100%
Binary sorting into buckets time: 00:01:24
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 4.13901e+08 (target: 543245711)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
Reserving size (543245712) 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 461325549
(Using difference cover)
Sorting block time: 00:03:52
Returning block of 461325550
Getting block 2 of 7
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:34
Sorting block of length 164721907
(Using difference cover)
Sorting block time: 00:01:19
Returning block of 164721908
Getting block 3 of 7
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:38
Sorting block of length 504364999
(Using difference cover)
Sorting block time: 00:04:26
Returning block of 504365000
Getting block 4 of 7
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:43
Sorting block of length 449050841
(Using difference cover)
Sorting block time: 00:04:03
Returning block of 449050842
Getting block 5 of 7
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:45
Sorting block of length 498817230
(Using difference cover)
Sorting block time: 00:04:34
Returning block of 498817231
Getting block 6 of 7
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:41
Sorting block of length 349103213
(Using difference cover)
Sorting block time: 00:02:57
Returning block of 349103214
Getting block 7 of 7
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:30
Sorting block of length 469926717
(Using difference cover)
Sorting block time: 00:04:10
Returning block of 469926718
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 854963149
fchr[G]: 1447929873
fchr[T]: 2041255101
fchr[$]: 2897310462
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 969972412 bytes to primary EBWT file: /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt.1.bt2
Wrote 724327620 bytes to secondary EBWT file: /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2897310462
bwtLen: 2897310463
sz: 724327616
bwtSz: 724327616
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 181081904
offsSz: 724327616
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 15090159
numLines: 15090159
ebwtTotLen: 965770176
ebwtTotSz: 965770176
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:42:16
Reading reference sizes
Time reading reference sizes: 00:00:24
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:20
Time to reverse reference sequence: 00:00:02
bmax according to bmaxDivN setting: 724327615
Using parameters --bmax 543245712 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 543245712 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:56
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:12
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:29
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: 00:01:41
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 3.62164e+08 (target: 543245711)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (543245712) 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 326094688
(Using difference cover)
Sorting block time: 00:02:40
Returning block of 326094689
Getting block 2 of 8
Reserving size (543245712) 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 262993484
(Using difference cover)
Sorting block time: 00:02:15
Returning block of 262993485
Getting block 3 of 8
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:38
Sorting block of length 378977620
(Using difference cover)
Sorting block time: 00:03:13
Returning block of 378977621
Getting block 4 of 8
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:38
Sorting block of length 275273737
(Using difference cover)
Sorting block time: 00:02:26
Returning block of 275273738
Getting block 5 of 8
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:44
Sorting block of length 489414676
(Using difference cover)
Sorting block time: 00:04:25
Returning block of 489414677
Getting block 6 of 8
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:44
Sorting block of length 386331170
(Using difference cover)
Sorting block time: 00:03:23
Returning block of 386331171
Getting block 7 of 8
Reserving size (543245712) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:42
Sorting block of length 393084325
(Using difference cover)
Sorting block time: 00:03:23
Returning block of 393084326
Getting block 8 of 8
Reserving size (543245712) 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 385140755
(Using difference cover)
Sorting block time: 00:03:17
Returning block of 385140756
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 854963149
fchr[G]: 1447929873
fchr[T]: 2041255101
fchr[$]: 2897310462
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 969972412 bytes to primary EBWT file: /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt.rev.1.bt2
Wrote 724327620 bytes to secondary EBWT file: /project2/NextGenMapTest/Teaser/references/GRCh37.fa_bt.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 2897310462
bwtLen: 2897310463
sz: 724327616
bwtSz: 724327616
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 181081904
offsSz: 724327616
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 15090159
numLines: 15090159
ebwtTotLen: 965770176
ebwtTotSz: 965770176
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:39:12