Settings:
Output files: "/project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_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/d_melanogaster.fasta
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:00:01
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:01
bmax according to bmaxDivN setting: 35643254
Using parameters --bmax 26732441 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 26732441 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:03
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: 00:00:01
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: 00:00:05
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:05
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:04
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: 00:00:05
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 1.78216e+07 (target: 26732440)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 10291629
(Using difference cover)
Sorting block time: 00:00:04
Returning block of 10291630
Getting block 2 of 8
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 17884072
(Using difference cover)
Sorting block time: 00:00:08
Returning block of 17884073
Getting block 3 of 8
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 11845640
(Using difference cover)
Sorting block time: 00:00:05
Returning block of 11845641
Getting block 4 of 8
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 23535943
(Using difference cover)
Sorting block time: 00:00:09
Returning block of 23535944
Getting block 5 of 8
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 25546130
(Using difference cover)
Sorting block time: 00:00:10
Returning block of 25546131
Getting block 6 of 8
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 24195086
(Using difference cover)
Sorting block time: 00:00:10
Returning block of 24195087
Getting block 7 of 8
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 15510888
(Using difference cover)
Sorting block time: 00:00:06
Returning block of 15510889
Getting block 8 of 8
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 13763622
(Using difference cover)
Sorting block time: 00:00:06
Returning block of 13763623
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 41351059
fchr[G]: 71311743
fchr[T]: 101240555
fchr[$]: 142573017
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 51892598 bytes to primary EBWT file: /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt.1.bt2
Wrote 35643260 bytes to secondary EBWT file: /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 142573017
bwtLen: 142573018
sz: 35643255
bwtSz: 35643255
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 8910814
offsSz: 35643256
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 742568
numLines: 742568
ebwtTotLen: 47524352
ebwtTotSz: 47524352
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:01:46
Reading reference sizes
Time reading reference sizes: 00:00:01
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:01
Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 35643254
Using parameters --bmax 26732441 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 26732441 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:03
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: 00:00:01
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: 00:00:05
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 2.03676e+07 (target: 26732440)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 18299241
(Using difference cover)
Sorting block time: 00:00:08
Returning block of 18299242
Getting block 2 of 7
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 26126377
(Using difference cover)
Sorting block time: 00:00:11
Returning block of 26126378
Getting block 3 of 7
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 21131594
(Using difference cover)
Sorting block time: 00:00:08
Returning block of 21131595
Getting block 4 of 7
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 22948118
(Using difference cover)
Sorting block time: 00:00:09
Returning block of 22948119
Getting block 5 of 7
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 21030658
(Using difference cover)
Sorting block time: 00:00:08
Returning block of 21030659
Getting block 6 of 7
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 21802436
(Using difference cover)
Sorting block time: 00:00:09
Returning block of 21802437
Getting block 7 of 7
Reserving size (26732441) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:02
Sorting block of length 11234587
(Using difference cover)
Sorting block time: 00:00:04
Returning block of 11234588
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 41351059
fchr[G]: 71311743
fchr[T]: 101240555
fchr[$]: 142573017
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 51892598 bytes to primary EBWT file: /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt.rev.1.bt2
Wrote 35643260 bytes to secondary EBWT file: /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta_bt.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 142573017
bwtLen: 142573018
sz: 35643255
bwtSz: 35643255
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 8910814
offsSz: 35643256
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 742568
numLines: 742568
ebwtTotLen: 47524352
ebwtTotSz: 47524352
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:01:31