Settings: Output files: "/projects/NBL/HS1795/700B4AAXX_2/tophat/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/HS1795/700B4AAXX_2/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:01:31 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:26 bmax according to bmaxDivN setting: 101231742 Using parameters --bmax 75923807 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 75923807 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:18 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:04 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:08 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: 00:00:26 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.06159e+07 (target: 75923806) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (75923807) 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 38872405 (Using difference cover) Sorting block time: 00:00:31 Returning block of 38872406 Getting block 2 of 8 Reserving size (75923807) 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 51147407 (Using difference cover) Sorting block time: 00:00:45 Returning block of 51147408 Getting block 3 of 8 Reserving size (75923807) 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 32666308 (Using difference cover) Sorting block time: 00:00:28 Returning block of 32666309 Getting block 4 of 8 Reserving size (75923807) 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 47956135 (Using difference cover) Sorting block time: 00:00:44 Returning block of 47956136 Getting block 5 of 8 Reserving size (75923807) 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: 00:00:14 Sorting block of length 53757385 (Using difference cover) Sorting block time: 00:00:48 Returning block of 53757386 Getting block 6 of 8 Reserving size (75923807) 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: 00:00:14 Sorting block of length 61684416 (Using difference cover) Sorting block time: 00:00:58 Returning block of 61684417 Getting block 7 of 8 Reserving size (75923807) 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 52314675 (Using difference cover) Sorting block time: 00:00:45 Returning block of 52314676 Getting block 8 of 8 Reserving size (75923807) 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 66528230 (Using difference cover) Sorting block time: 00:00:57 Returning block of 66528231 Exited Ebwt loop fchr[A]: 0 fchr[C]: 101437755 fchr[G]: 200642400 fchr[T]: 299865500 fchr[$]: 404926968 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 735837949 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_2/tophat/tmp/segment_juncs.1.ebwt Wrote 50615876 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_2/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 404926968 bwtLen: 404926969 sz: 101231742 bwtSz: 101231743 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12653968 offsSz: 50615872 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 903855 numSides: 1807710 numLines: 1807710 ebwtTotLen: 115693440 ebwtTotSz: 115693440 Total time for call to driver() for forward index: 00:13:01 Reading reference sizes Time reading reference sizes: 00:00:05 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: 101231742 Using parameters --bmax 75923807 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 75923807 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:18 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: 00:00:08 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: 00:00:35 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.78467e+07 (target: 75923806) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (75923807) 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 51734554 (Using difference cover) Sorting block time: 00:00:41 Returning block of 51734555 Getting block 2 of 7 Reserving size (75923807) 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 74923158 (Using difference cover) Sorting block time: 00:01:04 Returning block of 74923159 Getting block 3 of 7 Reserving size (75923807) 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 48151313 (Using difference cover) Sorting block time: 00:00:44 Returning block of 48151314 Getting block 4 of 7 Reserving size (75923807) 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: 00:00:14 Sorting block of length 73267562 (Using difference cover) Sorting block time: 00:01:05 Returning block of 73267563 Getting block 5 of 7 Reserving size (75923807) 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: 00:00:14 Sorting block of length 73738092 (Using difference cover) Sorting block time: 00:01:05 Returning block of 73738093 Getting block 6 of 7 Reserving size (75923807) 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: 00:00:14 Sorting block of length 36345198 (Using difference cover) Sorting block time: 00:00:34 Returning block of 36345199 Getting block 7 of 7 Reserving size (75923807) 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 46767085 (Using difference cover) Sorting block time: 00:00:40 Returning block of 46767086 Exited Ebwt loop fchr[A]: 0 fchr[C]: 101437755 fchr[G]: 200642400 fchr[T]: 299865500 fchr[$]: 404926968 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 735837949 bytes to primary EBWT file: /projects/NBL/HS1795/700B4AAXX_2/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 50615876 bytes to secondary EBWT file: /projects/NBL/HS1795/700B4AAXX_2/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 404926968 bwtLen: 404926969 sz: 101231742 bwtSz: 101231743 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12653968 offsSz: 50615872 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 903855 numSides: 1807710 numLines: 1807710 ebwtTotLen: 115693440 ebwtTotSz: 115693440 Total time for backward call to driver() for mirror index: 00:10:55