Settings: Output files: "/projects/NBL/HS1194/311L9AAXX_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/HS1194/311L9AAXX_4/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:13 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:10 bmax according to bmaxDivN setting: 40170011 Using parameters --bmax 30127509 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 30127509 --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: 00:00:14 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 5; 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: 2.0085e+07 (target: 30127508) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (30127509) 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 7988221 (Using difference cover) Sorting block time: 00:00:06 Returning block of 7988222 Getting block 2 of 8 Reserving size (30127509) 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 27994094 (Using difference cover) Sorting block time: 00:00:36 Returning block of 27994095 Getting block 3 of 8 Reserving size (30127509) 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 16938000 (Using difference cover) Sorting block time: 00:00:22 Returning block of 16938001 Getting block 4 of 8 Reserving size (30127509) 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 23043453 (Using difference cover) Sorting block time: 00:00:32 Returning block of 23043454 Getting block 5 of 8 Reserving size (30127509) 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 19961751 (Using difference cover) Sorting block time: 00:00:25 Returning block of 19961752 Getting block 6 of 8 Reserving size (30127509) 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 21259626 (Using difference cover) Sorting block time: 00:00:31 Returning block of 21259627 Getting block 7 of 8 Reserving size (30127509) 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 18350847 (Using difference cover) Sorting block time: 00:00:23 Returning block of 18350848 Getting block 8 of 8 Reserving size (30127509) 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 25144045 (Using difference cover) Sorting block time: 00:00:28 Returning block of 25144046 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41154860 fchr[G]: 80964137 fchr[T]: 119109582 fchr[$]: 160680044 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 294500857 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_4/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 20085012 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_4/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 160680044 bwtLen: 160680045 sz: 40170011 bwtSz: 40170012 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5021252 offsSz: 20085008 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 358661 numSides: 717322 numLines: 717322 ebwtTotLen: 45908608 ebwtTotSz: 45908608 Total time for call to driver() for forward index: 00:05:27 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: 00:00:09 bmax according to bmaxDivN setting: 40170011 Using parameters --bmax 30127509 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 30127509 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:07 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: 00:00:12 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; 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 Split 2, merged 1; 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 Split 2, merged 2; 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: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.0085e+07 (target: 30127508) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (30127509) 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 22696774 (Using difference cover) Sorting block time: 00:00:24 Returning block of 22696775 Getting block 2 of 8 Reserving size (30127509) 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 13954685 (Using difference cover) Sorting block time: 00:00:17 Returning block of 13954686 Getting block 3 of 8 Reserving size (30127509) 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 16972867 (Using difference cover) Sorting block time: 00:00:21 Returning block of 16972868 Getting block 4 of 8 Reserving size (30127509) 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 17769165 (Using difference cover) Sorting block time: 00:00:23 Returning block of 17769166 Getting block 5 of 8 Reserving size (30127509) 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 14112207 (Using difference cover) Sorting block time: 00:00:18 Returning block of 14112208 Getting block 6 of 8 Reserving size (30127509) 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 23711271 (Using difference cover) Sorting block time: 00:00:33 Returning block of 23711272 Getting block 7 of 8 Reserving size (30127509) 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 28020301 (Using difference cover) Sorting block time: 00:00:35 Returning block of 28020302 Getting block 8 of 8 Reserving size (30127509) 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 23442767 (Using difference cover) Sorting block time: 00:00:27 Returning block of 23442768 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41154860 fchr[G]: 80964137 fchr[T]: 119109582 fchr[$]: 160680044 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 294500857 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_4/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 20085012 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_4/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 160680044 bwtLen: 160680045 sz: 40170011 bwtSz: 40170012 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5021252 offsSz: 20085008 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 358661 numSides: 717322 numLines: 717322 ebwtTotLen: 45908608 ebwtTotSz: 45908608 Total time for backward call to driver() for mirror index: 00:05:40