Settings: Output files: "/projects/NBL/HS1801/61074AAXX_8/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/HS1801/61074AAXX_8/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:01:18 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: 101674595 Using parameters --bmax 76255947 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 76255947 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:16 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: 00:00:06 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: 00:00:32 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.08373e+07 (target: 76255946) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (76255947) 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 74965567 (Using difference cover) Sorting block time: 00:01:04 Returning block of 74965568 Getting block 2 of 8 Reserving size (76255947) 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 20490656 (Using difference cover) Sorting block time: 00:00:17 Returning block of 20490657 Getting block 3 of 8 Reserving size (76255947) 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 70791851 (Using difference cover) Sorting block time: 00:01:05 Returning block of 70791852 Getting block 4 of 8 Reserving size (76255947) 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 29687218 (Using difference cover) Sorting block time: 00:00:26 Returning block of 29687219 Getting block 5 of 8 Reserving size (76255947) 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 75161316 (Using difference cover) Sorting block time: 00:01:09 Returning block of 75161317 Getting block 6 of 8 Reserving size (76255947) 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 50776841 (Using difference cover) Sorting block time: 00:00:44 Returning block of 50776842 Getting block 7 of 8 Reserving size (76255947) 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 62545764 (Using difference cover) Sorting block time: 00:00:54 Returning block of 62545765 Getting block 8 of 8 Reserving size (76255947) 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 22279160 (Using difference cover) Sorting block time: 00:00:17 Returning block of 22279161 Exited Ebwt loop fchr[A]: 0 fchr[C]: 101209311 fchr[G]: 201896209 fchr[T]: 302193456 fchr[$]: 406698380 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 738541355 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_8/tophat/tmp/segment_juncs.1.ebwt Wrote 50837304 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_8/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 406698380 bwtLen: 406698381 sz: 101674595 bwtSz: 101674596 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12709325 offsSz: 50837300 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 907809 numSides: 1815618 numLines: 1815618 ebwtTotLen: 116199552 ebwtTotSz: 116199552 Total time for call to driver() for forward index: 00:11:28 Reading reference sizes Time reading reference sizes: 00:00:06 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: 101674595 Using parameters --bmax 76255947 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 76255947 --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: 00:00:06 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: 5.08373e+07 (target: 76255946) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (76255947) 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 20354247 (Using difference cover) Sorting block time: 00:00:15 Returning block of 20354248 Getting block 2 of 8 Reserving size (76255947) 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 66154887 (Using difference cover) Sorting block time: 00:00:57 Returning block of 66154888 Getting block 3 of 8 Reserving size (76255947) 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 43663682 (Using difference cover) Sorting block time: 00:00:37 Returning block of 43663683 Getting block 4 of 8 Reserving size (76255947) 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 33906279 (Using difference cover) Sorting block time: 00:00:32 Returning block of 33906280 Getting block 5 of 8 Reserving size (76255947) 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 61542472 (Using difference cover) Sorting block time: 00:00:55 Returning block of 61542473 Getting block 6 of 8 Reserving size (76255947) 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 58174955 (Using difference cover) Sorting block time: 00:00:54 Returning block of 58174956 Getting block 7 of 8 Reserving size (76255947) 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 75258846 (Using difference cover) Sorting block time: 00:01:06 Returning block of 75258847 Getting block 8 of 8 Reserving size (76255947) 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 47643005 (Using difference cover) Sorting block time: 00:00:40 Returning block of 47643006 Exited Ebwt loop fchr[A]: 0 fchr[C]: 101209311 fchr[G]: 201896209 fchr[T]: 302193456 fchr[$]: 406698380 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 738541355 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_8/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 50837304 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_8/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 406698380 bwtLen: 406698381 sz: 101674595 bwtSz: 101674596 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12709325 offsSz: 50837300 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 907809 numSides: 1815618 numLines: 1815618 ebwtTotLen: 116199552 ebwtTotSz: 116199552 Total time for backward call to driver() for mirror index: 00:10:44