Settings: Output files: "/projects/NBL/HS1799/61074AAXX_5/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/HS1799/61074AAXX_5/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:01:21 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: 100456486 Using parameters --bmax 75342365 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 75342365 --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: 00:00:04 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: 00:00:31 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.74037e+07 (target: 75342364) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (75342365) 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 74019113 (Using difference cover) Sorting block time: 00:01:04 Returning block of 74019114 Getting block 2 of 7 Reserving size (75342365) 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 46979467 (Using difference cover) Sorting block time: 00:00:38 Returning block of 46979468 Getting block 3 of 7 Reserving size (75342365) 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 33654322 (Using difference cover) Sorting block time: 00:00:29 Returning block of 33654323 Getting block 4 of 7 Reserving size (75342365) 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 74561074 (Using difference cover) Sorting block time: 00:01:09 Returning block of 74561075 Getting block 5 of 7 Reserving size (75342365) 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 73429284 (Using difference cover) Sorting block time: 00:01:04 Returning block of 73429285 Getting block 6 of 7 Reserving size (75342365) 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 34566759 (Using difference cover) Sorting block time: 00:00:28 Returning block of 34566760 Getting block 7 of 7 Reserving size (75342365) 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 64615920 (Using difference cover) Sorting block time: 00:00:55 Returning block of 64615921 Exited Ebwt loop fchr[A]: 0 fchr[C]: 99627002 fchr[G]: 199689186 fchr[T]: 298894720 fchr[$]: 401825945 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 730292822 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_5/tophat/tmp/segment_juncs.1.ebwt Wrote 50228248 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_5/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 401825945 bwtLen: 401825946 sz: 100456487 bwtSz: 100456487 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12557061 offsSz: 50228244 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 896933 numSides: 1793866 numLines: 1793866 ebwtTotLen: 114807424 ebwtTotSz: 114807424 Total time for call to driver() for forward index: 00:11:56 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: 100456486 Using parameters --bmax 75342365 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 75342365 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:14 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 Avg bucket size: 5.74037e+07 (target: 75342364) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (75342365) 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 49363989 (Using difference cover) Sorting block time: 00:00:37 Returning block of 49363990 Getting block 2 of 7 Reserving size (75342365) 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 66163934 (Using difference cover) Sorting block time: 00:00:53 Returning block of 66163935 Getting block 3 of 7 Reserving size (75342365) 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 66767367 (Using difference cover) Sorting block time: 00:00:58 Returning block of 66767368 Getting block 4 of 7 Reserving size (75342365) 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 44823007 (Using difference cover) Sorting block time: 00:00:39 Returning block of 44823008 Getting block 5 of 7 Reserving size (75342365) 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 48366339 (Using difference cover) Sorting block time: 00:00:42 Returning block of 48366340 Getting block 6 of 7 Reserving size (75342365) 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 63970390 (Using difference cover) Sorting block time: 00:00:52 Returning block of 63970391 Getting block 7 of 7 Reserving size (75342365) 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 62370913 (Using difference cover) Sorting block time: 00:00:50 Returning block of 62370914 Exited Ebwt loop fchr[A]: 0 fchr[C]: 99627002 fchr[G]: 199689186 fchr[T]: 298894720 fchr[$]: 401825945 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 730292822 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_5/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 50228248 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_5/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 401825945 bwtLen: 401825946 sz: 100456487 bwtSz: 100456487 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12557061 offsSz: 50228244 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 896933 numSides: 1793866 numLines: 1793866 ebwtTotLen: 114807424 ebwtTotSz: 114807424 Total time for backward call to driver() for mirror index: 00:10:19