Settings: Output files: "/projects/NBL/HS1801/61074AAXX_6/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/HS1801/61074AAXX_6/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:43 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: 103245784 Using parameters --bmax 77434338 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 77434338 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:16 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: 00:00:06 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: 00:00:34 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: 00:00:22 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: 00:00:25 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 0; 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: 5.16229e+07 (target: 77434337) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (77434338) 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 59009388 (Using difference cover) Sorting block time: 00:00:47 Returning block of 59009389 Getting block 2 of 8 Reserving size (77434338) 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 48851445 (Using difference cover) Sorting block time: 00:00:41 Returning block of 48851446 Getting block 3 of 8 Reserving size (77434338) 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: 00:00:11 Sorting block of length 67484190 (Using difference cover) Sorting block time: 00:01:01 Returning block of 67484191 Getting block 4 of 8 Reserving size (77434338) 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 61230118 (Using difference cover) Sorting block time: 00:00:52 Returning block of 61230119 Getting block 5 of 8 Reserving size (77434338) 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 29095886 (Using difference cover) Sorting block time: 00:00:26 Returning block of 29095887 Getting block 6 of 8 Reserving size (77434338) 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 67823760 (Using difference cover) Sorting block time: 00:00:58 Returning block of 67823761 Getting block 7 of 8 Reserving size (77434338) 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 49726493 (Using difference cover) Sorting block time: 00:00:42 Returning block of 49726494 Getting block 8 of 8 Reserving size (77434338) 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 29761849 (Using difference cover) Sorting block time: 00:00:23 Returning block of 29761850 Exited Ebwt loop fchr[A]: 0 fchr[C]: 102705762 fchr[G]: 204895751 fchr[T]: 306925868 fchr[$]: 412983136 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 749898596 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_6/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 51622900 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_6/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 412983136 bwtLen: 412983137 sz: 103245784 bwtSz: 103245785 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12905724 offsSz: 51622896 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 921838 numSides: 1843676 numLines: 1843676 ebwtTotLen: 117995264 ebwtTotSz: 117995264 Total time for call to driver() for forward index: 00:12:02 Reading reference sizes Time reading reference sizes: 00:00:07 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: 103245784 Using parameters --bmax 77434338 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 77434338 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:16 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: 00:00:07 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: 00:00:32 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 Avg bucket size: 5.89976e+07 (target: 77434337) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (77434338) 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 45186837 (Using difference cover) Sorting block time: 00:00:36 Returning block of 45186838 Getting block 2 of 7 Reserving size (77434338) 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: 00:00:11 Sorting block of length 75538752 (Using difference cover) Sorting block time: 00:01:04 Returning block of 75538753 Getting block 3 of 7 Reserving size (77434338) 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: 00:00:11 Sorting block of length 46886805 (Using difference cover) Sorting block time: 00:00:43 Returning block of 46886806 Getting block 4 of 7 Reserving size (77434338) 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 68124885 (Using difference cover) Sorting block time: 00:00:59 Returning block of 68124886 Getting block 5 of 7 Reserving size (77434338) 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 52615459 (Using difference cover) Sorting block time: 00:00:48 Returning block of 52615460 Getting block 6 of 7 Reserving size (77434338) 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 74122758 (Using difference cover) Sorting block time: 00:01:03 Returning block of 74122759 Getting block 7 of 7 Reserving size (77434338) 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 50507634 (Using difference cover) Sorting block time: 00:00:41 Returning block of 50507635 Exited Ebwt loop fchr[A]: 0 fchr[C]: 102705762 fchr[G]: 204895751 fchr[T]: 306925868 fchr[$]: 412983136 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 749898596 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_6/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 51622900 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_6/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 412983136 bwtLen: 412983137 sz: 103245784 bwtSz: 103245785 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12905724 offsSz: 51622896 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 921838 numSides: 1843676 numLines: 1843676 ebwtTotLen: 117995264 ebwtTotSz: 117995264 Total time for backward call to driver() for mirror index: 00:10:28