Settings: Output files: "/projects/NBL/HS1799/61B1HAAXX_7/tophat_wj/tmp/segment_juncs.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) 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: /projects/NBL/HS1799/61B1HAAXX_7/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:43 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:25 bmax according to bmaxDivN setting: 102078801 Using parameters --bmax 76559101 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 76559101 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:15 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:07 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: 00:00:38 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:27 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:25 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:27 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:26 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Avg bucket size: 4.53684e+07 (target: 76559100) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:08 Sorting block of length 49383156 (Using difference cover) Sorting block time: 00:00:37 Returning block of 49383157 Getting block 2 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:11 Sorting block of length 78808301 (Using difference cover) Sorting block time: 00:01:05 Returning block of 78808302 Getting block 3 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:10 Sorting block of length 1 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2 Getting block 4 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:10 Sorting block of length 29185045 (Using difference cover) Sorting block time: 00:00:26 Returning block of 29185046 Getting block 5 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:13 Sorting block of length 73857740 (Using difference cover) Sorting block time: 00:01:03 Returning block of 73857741 Getting block 6 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:12 Sorting block of length 35854210 (Using difference cover) Sorting block time: 00:00:32 Returning block of 35854211 Getting block 7 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:13 Sorting block of length 42650172 (Using difference cover) Sorting block time: 00:00:35 Returning block of 42650173 Getting block 8 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:13 Sorting block of length 60586891 (Using difference cover) Sorting block time: 00:00:50 Returning block of 60586892 Getting block 9 of 9 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:09 Sorting block of length 37989680 (Using difference cover) Sorting block time: 00:00:29 Returning block of 37989681 Exited Ebwt loop fchr[A]: 0 fchr[C]: 101360428 fchr[G]: 202675536 fchr[T]: 303528392 fchr[$]: 408315204 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 742190283 bytes to primary EBWT file: /projects/NBL/HS1799/61B1HAAXX_7/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 51039408 bytes to secondary EBWT file: /projects/NBL/HS1799/61B1HAAXX_7/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 408315204 bwtLen: 408315205 sz: 102078801 bwtSz: 102078802 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12759851 offsSz: 51039404 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 911418 numSides: 1822836 numLines: 1822836 ebwtTotLen: 116661504 ebwtTotSz: 116661504 Total time for call to driver() for forward index: 00:12:22 Reading reference sizes Time reading reference sizes: 00:00:08 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:25 bmax according to bmaxDivN setting: 102078801 Using parameters --bmax 76559101 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 76559101 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:15 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:07 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: 00:00:34 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:25 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.83307e+07 (target: 76559100) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:08 Sorting block of length 71650258 (Using difference cover) Sorting block time: 00:00:55 Returning block of 71650259 Getting block 2 of 7 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:11 Sorting block of length 62558796 (Using difference cover) Sorting block time: 00:00:49 Returning block of 62558797 Getting block 3 of 7 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:11 Sorting block of length 42432342 (Using difference cover) Sorting block time: 00:00:37 Returning block of 42432343 Getting block 4 of 7 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:13 Sorting block of length 52756399 (Using difference cover) Sorting block time: 00:00:42 Returning block of 52756400 Getting block 5 of 7 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:13 Sorting block of length 69101383 (Using difference cover) Sorting block time: 00:01:02 Returning block of 69101384 Getting block 6 of 7 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:15 Sorting block of length 37320613 (Using difference cover) Sorting block time: 00:00:30 Returning block of 37320614 Getting block 7 of 7 Reserving size (76559101) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:09 Sorting block of length 72495407 (Using difference cover) Sorting block time: 00:00:59 Returning block of 72495408 Exited Ebwt loop fchr[A]: 0 fchr[C]: 101360428 fchr[G]: 202675536 fchr[T]: 303528392 fchr[$]: 408315204 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 742190283 bytes to primary EBWT file: /projects/NBL/HS1799/61B1HAAXX_7/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 51039408 bytes to secondary EBWT file: /projects/NBL/HS1799/61B1HAAXX_7/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 408315204 bwtLen: 408315205 sz: 102078801 bwtSz: 102078802 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12759851 offsSz: 51039404 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 911418 numSides: 1822836 numLines: 1822836 ebwtTotLen: 116661504 ebwtTotSz: 116661504 Total time for backward call to driver() for mirror index: 00:10:09