Settings: Output files: "/projects/NBL/HS1803/616GYAAXX_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/HS1803/616GYAAXX_4/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:02:12 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:26 bmax according to bmaxDivN setting: 101321165 Using parameters --bmax 75990874 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 75990874 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:19 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: 00:00:25 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.06606e+07 (target: 75990873) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (75990874) 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 29137005 (Using difference cover) Sorting block time: 00:00:24 Returning block of 29137006 Getting block 2 of 8 Reserving size (75990874) 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 50594807 (Using difference cover) Sorting block time: 00:00:47 Returning block of 50594808 Getting block 3 of 8 Reserving size (75990874) 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 33890945 (Using difference cover) Sorting block time: 00:00:31 Returning block of 33890946 Getting block 4 of 8 Reserving size (75990874) 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 72583577 (Using difference cover) Sorting block time: 00:01:13 Returning block of 72583578 Getting block 5 of 8 Reserving size (75990874) 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 59498771 (Using difference cover) Sorting block time: 00:00:59 Returning block of 59498772 Getting block 6 of 8 Reserving size (75990874) 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 72252723 (Using difference cover) Sorting block time: 00:01:11 Returning block of 72252724 Getting block 7 of 8 Reserving size (75990874) 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 51405120 (Using difference cover) Sorting block time: 00:00:48 Returning block of 51405121 Getting block 8 of 8 Reserving size (75990874) 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 35921705 (Using difference cover) Sorting block time: 00:00:31 Returning block of 35921706 Exited Ebwt loop fchr[A]: 0 fchr[C]: 103137464 fchr[G]: 201370775 fchr[T]: 298798883 fchr[$]: 405284660 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 736431194 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_4/tophat/tmp/segment_juncs.1.ebwt Wrote 50660588 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_4/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 405284660 bwtLen: 405284661 sz: 101321165 bwtSz: 101321166 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12665146 offsSz: 50660584 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 904654 numSides: 1809308 numLines: 1809308 ebwtTotLen: 115795712 ebwtTotSz: 115795712 Total time for call to driver() for forward index: 00:13:57 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: 101321165 Using parameters --bmax 75990874 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 75990874 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:18 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: 00:00:07 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: 00:00:33 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: 00:00:29 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.06606e+07 (target: 75990873) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (75990874) 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 7416883 (Using difference cover) Sorting block time: 00:00:06 Returning block of 7416884 Getting block 2 of 8 Reserving size (75990874) 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 70141799 (Using difference cover) Sorting block time: 00:01:06 Returning block of 70141800 Getting block 3 of 8 Reserving size (75990874) 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 74717818 (Using difference cover) Sorting block time: 00:01:14 Returning block of 74717819 Getting block 4 of 8 Reserving size (75990874) 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 58213143 (Using difference cover) Sorting block time: 00:00:57 Returning block of 58213144 Getting block 5 of 8 Reserving size (75990874) 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 67309654 (Using difference cover) Sorting block time: 00:01:09 Returning block of 67309655 Getting block 6 of 8 Reserving size (75990874) 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 22803909 (Using difference cover) Sorting block time: 00:00:21 Returning block of 22803910 Getting block 7 of 8 Reserving size (75990874) 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 74177224 (Using difference cover) Sorting block time: 00:01:09 Returning block of 74177225 Getting block 8 of 8 Reserving size (75990874) 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 30504223 (Using difference cover) Sorting block time: 00:00:26 Returning block of 30504224 Exited Ebwt loop fchr[A]: 0 fchr[C]: 103137464 fchr[G]: 201370775 fchr[T]: 298798883 fchr[$]: 405284660 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 736431194 bytes to primary EBWT file: /projects/NBL/HS1803/616GYAAXX_4/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 50660588 bytes to secondary EBWT file: /projects/NBL/HS1803/616GYAAXX_4/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 405284660 bwtLen: 405284661 sz: 101321165 bwtSz: 101321166 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12665146 offsSz: 50660584 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 904654 numSides: 1809308 numLines: 1809308 ebwtTotLen: 115795712 ebwtTotSz: 115795712 Total time for backward call to driver() for mirror index: 00:12:04