Settings: Output files: "/projects/NBL/HS1198/30UBRAAXX_7/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/HS1198/30UBRAAXX_7/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:10 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:08 bmax according to bmaxDivN setting: 37676559 Using parameters --bmax 28257420 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 28257420 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:06 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:02 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: 00:00:12 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:10 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 2; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:09 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: 00:00:09 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: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.88383e+07 (target: 28257419) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (28257420) 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: 00:00:03 Sorting block of length 24327718 (Using difference cover) Sorting block time: 00:00:24 Returning block of 24327719 Getting block 2 of 8 Reserving size (28257420) 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: 00:00:04 Sorting block of length 5159018 (Using difference cover) Sorting block time: 00:00:05 Returning block of 5159019 Getting block 3 of 8 Reserving size (28257420) 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: 00:00:04 Sorting block of length 24365904 (Using difference cover) Sorting block time: 00:00:30 Returning block of 24365905 Getting block 4 of 8 Reserving size (28257420) 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: 00:00:04 Sorting block of length 12124645 (Using difference cover) Sorting block time: 00:00:16 Returning block of 12124646 Getting block 5 of 8 Reserving size (28257420) 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: 00:00:05 Sorting block of length 17993358 (Using difference cover) Sorting block time: 00:00:19 Returning block of 17993359 Getting block 6 of 8 Reserving size (28257420) 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: 00:00:05 Sorting block of length 20306168 (Using difference cover) Sorting block time: 00:00:22 Returning block of 20306169 Getting block 7 of 8 Reserving size (28257420) 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: 00:00:05 Sorting block of length 24707379 (Using difference cover) Sorting block time: 00:00:29 Returning block of 24707380 Getting block 8 of 8 Reserving size (28257420) 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: 00:00:03 Sorting block of length 21722041 (Using difference cover) Sorting block time: 00:00:23 Returning block of 21722042 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41001398 fchr[G]: 76436851 fchr[T]: 109896523 fchr[$]: 150706238 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 276592008 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_7/tophat/tmp/segment_juncs.1.ebwt Wrote 18838284 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_7/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 150706238 bwtLen: 150706239 sz: 37676560 bwtSz: 37676560 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4709570 offsSz: 18838280 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 336398 numSides: 672796 numLines: 672796 ebwtTotLen: 43058944 ebwtTotSz: 43058944 Total time for call to driver() for forward index: 00:05:03 Reading reference sizes Time reading reference sizes: 00:00:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:12 bmax according to bmaxDivN setting: 37676559 Using parameters --bmax 28257420 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 28257420 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:08 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:03 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: 00:00:15 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:10 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.88383e+07 (target: 28257419) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (28257420) 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: 00:00:03 Sorting block of length 14831387 (Using difference cover) Sorting block time: 00:00:13 Returning block of 14831388 Getting block 2 of 8 Reserving size (28257420) 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: 00:00:03 Sorting block of length 19787623 (Using difference cover) Sorting block time: 00:00:23 Returning block of 19787624 Getting block 3 of 8 Reserving size (28257420) 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: 00:00:05 Sorting block of length 26776618 (Using difference cover) Sorting block time: 00:00:40 Returning block of 26776619 Getting block 4 of 8 Reserving size (28257420) 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: 00:00:07 Sorting block of length 24622810 (Using difference cover) Sorting block time: 00:00:35 Returning block of 24622811 Getting block 5 of 8 Reserving size (28257420) 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: 00:00:07 Sorting block of length 20764313 (Using difference cover) Sorting block time: 00:00:30 Returning block of 20764314 Getting block 6 of 8 Reserving size (28257420) 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: 00:00:07 Sorting block of length 9166484 (Using difference cover) Sorting block time: 00:00:14 Returning block of 9166485 Getting block 7 of 8 Reserving size (28257420) 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: 00:00:06 Sorting block of length 19353066 (Using difference cover) Sorting block time: 00:00:27 Returning block of 19353067 Getting block 8 of 8 Reserving size (28257420) 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: 00:00:04 Sorting block of length 15403930 (Using difference cover) Sorting block time: 00:00:20 Returning block of 15403931 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41001398 fchr[G]: 76436851 fchr[T]: 109896523 fchr[$]: 150706238 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 276592008 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_7/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 18838284 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_7/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 150706238 bwtLen: 150706239 sz: 37676560 bwtSz: 37676560 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4709570 offsSz: 18838280 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 336398 numSides: 672796 numLines: 672796 ebwtTotLen: 43058944 ebwtTotSz: 43058944 Total time for backward call to driver() for mirror index: 00:05:23