Settings: Output files: "/projects/NBL/HS1197/311NGAAXX_4/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/HS1197/311NGAAXX_4/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:27 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:15 bmax according to bmaxDivN setting: 56259217 Using parameters --bmax 42194413 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 42194413 --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: 00:00:03 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: 00:00:18 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 8; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:13 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: 00:00:13 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: 00:00:14 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.75061e+07 (target: 42194412) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (42194413) 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 41800320 (Using difference cover) Sorting block time: 00:01:05 Returning block of 41800321 Getting block 2 of 6 Reserving size (42194413) 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 34196628 (Using difference cover) Sorting block time: 00:01:00 Returning block of 34196629 Getting block 3 of 6 Reserving size (42194413) 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 41711626 (Using difference cover) Sorting block time: 00:01:16 Returning block of 41711627 Getting block 4 of 6 Reserving size (42194413) 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 32402465 (Using difference cover) Sorting block time: 00:00:55 Returning block of 32402466 Getting block 5 of 6 Reserving size (42194413) 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 36113616 (Using difference cover) Sorting block time: 00:01:06 Returning block of 36113617 Getting block 6 of 6 Reserving size (42194413) 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 38812209 (Using difference cover) Sorting block time: 00:01:02 Returning block of 38812210 Exited Ebwt loop fchr[A]: 0 fchr[C]: 59114934 fchr[G]: 112941300 fchr[T]: 165660003 fchr[$]: 225036869 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 411160340 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_4/tophat/tmp/segment_juncs.1.ebwt Wrote 28129616 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_4/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 225036869 bwtLen: 225036870 sz: 56259218 bwtSz: 56259218 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 7032403 offsSz: 28129612 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 502315 numSides: 1004630 numLines: 1004630 ebwtTotLen: 64296320 ebwtTotSz: 64296320 Total time for call to driver() for forward index: 00:10:35 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: 00:00:14 bmax according to bmaxDivN setting: 56259217 Using parameters --bmax 42194413 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 42194413 --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: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:05 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: 00:00:19 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 8; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:16 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: 00:00:15 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.81296e+07 (target: 42194412) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (42194413) 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 38338528 (Using difference cover) Sorting block time: 00:01:01 Returning block of 38338529 Getting block 2 of 8 Reserving size (42194413) 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 27908176 (Using difference cover) Sorting block time: 00:00:48 Returning block of 27908177 Getting block 3 of 8 Reserving size (42194413) 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 19465861 (Using difference cover) Sorting block time: 00:00:36 Returning block of 19465862 Getting block 4 of 8 Reserving size (42194413) 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 23213910 (Using difference cover) Sorting block time: 00:00:42 Returning block of 23213911 Getting block 5 of 8 Reserving size (42194413) 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 28768369 (Using difference cover) Sorting block time: 00:00:50 Returning block of 28768370 Getting block 6 of 8 Reserving size (42194413) 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 37754923 (Using difference cover) Sorting block time: 00:01:05 Returning block of 37754924 Getting block 7 of 8 Reserving size (42194413) 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 30833694 (Using difference cover) Sorting block time: 00:00:55 Returning block of 30833695 Getting block 8 of 8 Reserving size (42194413) 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 18753401 (Using difference cover) Sorting block time: 00:00:25 Returning block of 18753402 Exited Ebwt loop fchr[A]: 0 fchr[C]: 59114934 fchr[G]: 112941300 fchr[T]: 165660003 fchr[$]: 225036869 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 411160340 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_4/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 28129616 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_4/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 225036869 bwtLen: 225036870 sz: 56259218 bwtSz: 56259218 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 7032403 offsSz: 28129612 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 502315 numSides: 1004630 numLines: 1004630 ebwtTotLen: 64296320 ebwtTotSz: 64296320 Total time for backward call to driver() for mirror index: 00:10:31