Settings: Output files: "/projects/NBL/HS1801/61074AAXX_7/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_7/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:53 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: 103224320 Using parameters --bmax 77418240 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 77418240 --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: 00:00:04 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 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:26 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.16122e+07 (target: 77418239) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (77418240) 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 50586114 (Using difference cover) Sorting block time: 00:00:43 Returning block of 50586115 Getting block 2 of 8 Reserving size (77418240) 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 64897185 (Using difference cover) Sorting block time: 00:00:59 Returning block of 64897186 Getting block 3 of 8 Reserving size (77418240) 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 23715202 (Using difference cover) Sorting block time: 00:00:22 Returning block of 23715203 Getting block 4 of 8 Reserving size (77418240) 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 56783813 (Using difference cover) Sorting block time: 00:00:56 Returning block of 56783814 Getting block 5 of 8 Reserving size (77418240) 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 54135228 (Using difference cover) Sorting block time: 00:00:51 Returning block of 54135229 Getting block 6 of 8 Reserving size (77418240) 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 40406059 (Using difference cover) Sorting block time: 00:00:38 Returning block of 40406060 Getting block 7 of 8 Reserving size (77418240) 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 46183573 (Using difference cover) Sorting block time: 00:00:40 Returning block of 46183574 Getting block 8 of 8 Reserving size (77418240) 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 76190099 (Using difference cover) Sorting block time: 00:01:07 Returning block of 76190100 Exited Ebwt loop fchr[A]: 0 fchr[C]: 102901119 fchr[G]: 205132773 fchr[T]: 306887231 fchr[$]: 412897280 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 749664865 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_7/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 51612168 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_7/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 412897280 bwtLen: 412897281 sz: 103224320 bwtSz: 103224321 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12903041 offsSz: 51612164 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 921646 numSides: 1843292 numLines: 1843292 ebwtTotLen: 117970688 ebwtTotSz: 117970688 Total time for call to driver() for forward index: 00:12:00 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: 00:00:26 bmax according to bmaxDivN setting: 103224320 Using parameters --bmax 77418240 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 77418240 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:17 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: 00:00:08 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: 00:00:33 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; 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 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 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:27 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.16122e+07 (target: 77418239) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (77418240) 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 67845300 (Using difference cover) Sorting block time: 00:00:59 Returning block of 67845301 Getting block 2 of 8 Reserving size (77418240) 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 48328488 (Using difference cover) Sorting block time: 00:00:42 Returning block of 48328489 Getting block 3 of 8 Reserving size (77418240) 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 30679829 (Using difference cover) Sorting block time: 00:00:28 Returning block of 30679830 Getting block 4 of 8 Reserving size (77418240) 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 47283223 (Using difference cover) Sorting block time: 00:00:44 Returning block of 47283224 Getting block 5 of 8 Reserving size (77418240) 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 40546270 (Using difference cover) Sorting block time: 00:00:36 Returning block of 40546271 Getting block 6 of 8 Reserving size (77418240) 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 74280632 (Using difference cover) Sorting block time: 00:01:10 Returning block of 74280633 Getting block 7 of 8 Reserving size (77418240) 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 70539605 (Using difference cover) Sorting block time: 00:01:05 Returning block of 70539606 Getting block 8 of 8 Reserving size (77418240) 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 33393926 (Using difference cover) Sorting block time: 00:00:28 Returning block of 33393927 Exited Ebwt loop fchr[A]: 0 fchr[C]: 102901119 fchr[G]: 205132773 fchr[T]: 306887231 fchr[$]: 412897280 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 749664865 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_7/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 51612168 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_7/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 412897280 bwtLen: 412897281 sz: 103224320 bwtSz: 103224321 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12903041 offsSz: 51612164 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 921646 numSides: 1843292 numLines: 1843292 ebwtTotLen: 117970688 ebwtTotSz: 117970688 Total time for backward call to driver() for mirror index: 00:11:55