Settings:
Output files: "/project2/NextGenMapTest/Teaser/references/E_coli.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/E_coli.fasta
Building a SMALL index
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: 1283017
Using parameters --bmax 962263 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 962263 --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
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Binary sorting into buckets time: 00:00:00
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: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 733152 (target: 962262)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 583290
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 583291
Getting block 2 of 7
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 841267
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 841268
Getting block 3 of 7
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 953385
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 953386
Getting block 4 of 7
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 538875
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 538876
Getting block 5 of 7
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 949978
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 949979
Getting block 6 of 7
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 912888
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 912889
Getting block 7 of 7
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 352379
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 352380
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 1268010
fchr[G]: 2573696
fchr[T]: 3866403
fchr[$]: 5132068
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 5905266 bytes to primary EBWT file: /project2/NextGenMapTest/Teaser/references/E_coli.fasta_bt.1.bt2
Wrote 1283024 bytes to secondary EBWT file: /project2/NextGenMapTest/Teaser/references/E_coli.fasta_bt.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 5132068
bwtLen: 5132069
sz: 1283017
bwtSz: 1283018
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 320755
offsSz: 1283020
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 26730
numLines: 26730
ebwtTotLen: 1710720
ebwtTotSz: 1710720
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:00:02
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
Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 1283017
Using parameters --bmax 962263 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 962263 --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
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100%
Binary sorting into buckets time: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 5; iterating...
Binary sorting into buckets
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100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 641508 (target: 962262)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 245339
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 245340
Getting block 2 of 8
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 855428
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 855429
Getting block 3 of 8
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 880204
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 880205
Getting block 4 of 8
Reserving size (962263) 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 486769
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 486770
Getting block 5 of 8
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 739485
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 739486
Getting block 6 of 8
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 406763
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 406764
Getting block 7 of 8
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 904773
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 904774
Getting block 8 of 8
Reserving size (962263) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 613300
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 613301
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 1268010
fchr[G]: 2573696
fchr[T]: 3866403
fchr[$]: 5132068
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 5905266 bytes to primary EBWT file: /project2/NextGenMapTest/Teaser/references/E_coli.fasta_bt.rev.1.bt2
Wrote 1283024 bytes to secondary EBWT file: /project2/NextGenMapTest/Teaser/references/E_coli.fasta_bt.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 5132068
bwtLen: 5132069
sz: 1283017
bwtSz: 1283018
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 320755
offsSz: 1283020
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 26730
numLines: 26730
ebwtTotLen: 1710720
ebwtTotSz: 1710720
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:00:03