Settings: Output files: "CB_Testis_tp51/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: CB_Testis_tp51/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:01 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: 5160725 Using parameters --bmax 3870544 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3870544 --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 2, merged 5; 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: 2.94899e+06 (target: 3870543) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3870544) 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 2388268 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2388269 Getting block 2 of 7 Reserving size (3870544) 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 2652594 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2652595 Getting block 3 of 7 Reserving size (3870544) 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 3678834 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3678835 Getting block 4 of 7 Reserving size (3870544) 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 2622932 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2622933 Getting block 5 of 7 Reserving size (3870544) 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 3620639 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3620640 Getting block 6 of 7 Reserving size (3870544) 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 1896362 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1896363 Getting block 7 of 7 Reserving size (3870544) 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 3783268 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3783269 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5073311 fchr[G]: 10310183 fchr[T]: 15418279 fchr[$]: 20642903 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37830015 bytes to primary EBWT file: CB_Testis_tp51/tmp/segment_juncs.1.bt2 Wrote 5160732 bytes to secondary EBWT file: CB_Testis_tp51/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20642903 bwtLen: 20642904 sz: 5160726 bwtSz: 5160726 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1290182 offsSz: 5160728 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 107516 numLines: 107516 ebwtTotLen: 6881024 ebwtTotSz: 6881024 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:18 Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 5160725 Using parameters --bmax 3870544 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3870544 --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 Avg bucket size: 2.94899e+06 (target: 3870543) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3870544) 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 3702736 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3702737 Getting block 2 of 7 Reserving size (3870544) 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 2616974 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2616975 Getting block 3 of 7 Reserving size (3870544) 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 2871368 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2871369 Getting block 4 of 7 Reserving size (3870544) 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 2531192 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2531193 Getting block 5 of 7 Reserving size (3870544) 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 3283224 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3283225 Getting block 6 of 7 Reserving size (3870544) 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 3484560 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3484561 Getting block 7 of 7 Reserving size (3870544) 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 2152843 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2152844 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5073311 fchr[G]: 10310183 fchr[T]: 15418279 fchr[$]: 20642903 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37830015 bytes to primary EBWT file: CB_Testis_tp51/tmp/segment_juncs.rev.1.bt2 Wrote 5160732 bytes to secondary EBWT file: CB_Testis_tp51/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20642903 bwtLen: 20642904 sz: 5160726 bwtSz: 5160726 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1290182 offsSz: 5160728 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 107516 numLines: 107516 ebwtTotLen: 6881024 ebwtTotSz: 6881024 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17