Settings: Output files: "MCKidneyC12/tmp/segment_juncs.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) 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: MCKidneyC12/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 3892148 Using parameters --bmax 2919111 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2919111 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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: 00:00:01 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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.94607e+06 (target: 2919110) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2919111) 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: 00:00:01 Sorting block of length 2380165 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2380166 Getting block 2 of 8 Reserving size (2919111) 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: 00:00:01 Sorting block of length 1914242 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1914243 Getting block 3 of 8 Reserving size (2919111) 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: 00:00:01 Sorting block of length 2015389 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2015390 Getting block 4 of 8 Reserving size (2919111) 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: 00:00:01 Sorting block of length 2254892 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2254893 Getting block 5 of 8 Reserving size (2919111) 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: 00:00:00 Sorting block of length 2344598 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2344599 Getting block 6 of 8 Reserving size (2919111) 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: 00:00:00 Sorting block of length 1557793 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1557794 Getting block 7 of 8 Reserving size (2919111) 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: 00:00:00 Sorting block of length 2332322 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2332323 Getting block 8 of 8 Reserving size (2919111) 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: 00:00:00 Sorting block of length 769184 (Using difference cover) Sorting block time: 00:00:00 Returning block of 769185 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3747082 fchr[G]: 7812515 fchr[T]: 11653496 fchr[$]: 15568592 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 29581064 bytes to primary EBWT file: MCKidneyC12/tmp/segment_juncs.1.bt2 Wrote 3892156 bytes to secondary EBWT file: MCKidneyC12/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15568592 bwtLen: 15568593 sz: 3892148 bwtSz: 3892149 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 973038 offsSz: 3892152 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 81087 numLines: 81087 ebwtTotLen: 5189568 ebwtTotSz: 5189568 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:12 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 3892148 Using parameters --bmax 2919111 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2919111 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.22408e+06 (target: 2919110) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2919111) 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: 00:00:00 Sorting block of length 1604744 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1604745 Getting block 2 of 7 Reserving size (2919111) 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: 00:00:00 Sorting block of length 2472560 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2472561 Getting block 3 of 7 Reserving size (2919111) 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: 00:00:00 Sorting block of length 2128265 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2128266 Getting block 4 of 7 Reserving size (2919111) 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: 00:00:01 Sorting block of length 2913891 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2913892 Getting block 5 of 7 Reserving size (2919111) 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: 00:00:00 Sorting block of length 2708808 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2708809 Getting block 6 of 7 Reserving size (2919111) 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: 00:00:00 Sorting block of length 2751541 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2751542 Getting block 7 of 7 Reserving size (2919111) 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: 00:00:00 Sorting block of length 988777 (Using difference cover) Sorting block time: 00:00:01 Returning block of 988778 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3747082 fchr[G]: 7812515 fchr[T]: 11653496 fchr[$]: 15568592 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 29581064 bytes to primary EBWT file: MCKidneyC12/tmp/segment_juncs.rev.1.bt2 Wrote 3892156 bytes to secondary EBWT file: MCKidneyC12/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15568592 bwtLen: 15568593 sz: 3892148 bwtSz: 3892149 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 973038 offsSz: 3892152 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 81087 numLines: 81087 ebwtTotLen: 5189568 ebwtTotSz: 5189568 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:11