Settings: Output files: "/projects/NBL/HS1195/30TTYAAXX_4/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/HS1195/30TTYAAXX_4/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:39 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:22 bmax according to bmaxDivN setting: 90485705 Using parameters --bmax 67864279 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 67864279 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:23 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: 00:00:09 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 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:31 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.17061e+07 (target: 67864278) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (67864279) 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 38912566 (Using difference cover) Sorting block time: 00:00:44 Returning block of 38912567 Getting block 2 of 7 Reserving size (67864279) 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 65873151 (Using difference cover) Sorting block time: 00:01:37 Returning block of 65873152 Getting block 3 of 7 Reserving size (67864279) 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 48206707 (Using difference cover) Sorting block time: 00:01:17 Returning block of 48206708 Getting block 4 of 7 Reserving size (67864279) 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 65887587 (Using difference cover) Sorting block time: 00:01:42 Returning block of 65887588 Getting block 5 of 7 Reserving size (67864279) 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: 00:00:17 Sorting block of length 50218523 (Using difference cover) Sorting block time: 00:01:20 Returning block of 50218524 Getting block 6 of 7 Reserving size (67864279) 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: 00:00:17 Sorting block of length 64580752 (Using difference cover) Sorting block time: 00:01:41 Returning block of 64580753 Getting block 7 of 7 Reserving size (67864279) 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 28263530 (Using difference cover) Sorting block time: 00:00:34 Returning block of 28263531 Exited Ebwt loop fchr[A]: 0 fchr[C]: 99366789 fchr[G]: 180668102 fchr[T]: 261243926 fchr[$]: 361942822 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 658396276 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_4/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 45242860 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_4/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 361942822 bwtLen: 361942823 sz: 90485706 bwtSz: 90485706 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 11310714 offsSz: 45242856 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 807909 numSides: 1615818 numLines: 1615818 ebwtTotLen: 103412352 ebwtTotSz: 103412352 Total time for call to driver() for forward index: 00:14:37 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: 00:00:23 bmax according to bmaxDivN setting: 90485705 Using parameters --bmax 67864279 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 67864279 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:22 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:05 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: 00:00:32 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: 00:00:33 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 4.52429e+07 (target: 67864278) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (67864279) 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 58509276 (Using difference cover) Sorting block time: 00:01:16 Returning block of 58509277 Getting block 2 of 8 Reserving size (67864279) 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 43364880 (Using difference cover) Sorting block time: 00:01:03 Returning block of 43364881 Getting block 3 of 8 Reserving size (67864279) 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 63318691 (Using difference cover) Sorting block time: 00:01:40 Returning block of 63318692 Getting block 4 of 8 Reserving size (67864279) 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 23955820 (Using difference cover) Sorting block time: 00:00:36 Returning block of 23955821 Getting block 5 of 8 Reserving size (67864279) 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 49009765 (Using difference cover) Sorting block time: 00:01:18 Returning block of 49009766 Getting block 6 of 8 Reserving size (67864279) 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 42617320 (Using difference cover) Sorting block time: 00:01:05 Returning block of 42617321 Getting block 7 of 8 Reserving size (67864279) 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: 00:00:16 Sorting block of length 67829470 (Using difference cover) Sorting block time: 00:01:45 Returning block of 67829471 Getting block 8 of 8 Reserving size (67864279) 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 13337593 (Using difference cover) Sorting block time: 00:00:13 Returning block of 13337594 Exited Ebwt loop fchr[A]: 0 fchr[C]: 99366789 fchr[G]: 180668102 fchr[T]: 261243926 fchr[$]: 361942822 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 658396276 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_4/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 45242860 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_4/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 361942822 bwtLen: 361942823 sz: 90485706 bwtSz: 90485706 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 11310714 offsSz: 45242856 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 807909 numSides: 1615818 numLines: 1615818 ebwtTotLen: 103412352 ebwtTotSz: 103412352 Total time for backward call to driver() for mirror index: 00:14:49