Settings: Output files: "CB_Testis_tp172/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_tp172/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: 00:00:01 bmax according to bmaxDivN setting: 5335354 Using parameters --bmax 4001516 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4001516 --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: 00:00:01 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; 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: 2.66768e+06 (target: 4001515) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4001516) 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 1776100 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1776101 Getting block 2 of 8 Reserving size (4001516) 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 2809393 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2809394 Getting block 3 of 8 Reserving size (4001516) 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 2828828 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2828829 Getting block 4 of 8 Reserving size (4001516) 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 2551555 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2551556 Getting block 5 of 8 Reserving size (4001516) 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 3500080 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3500081 Getting block 6 of 8 Reserving size (4001516) 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 3438500 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3438501 Getting block 7 of 8 Reserving size (4001516) 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 1550305 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1550306 Getting block 8 of 8 Reserving size (4001516) 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 2886648 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2886649 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5267774 fchr[G]: 10713618 fchr[T]: 15908292 fchr[$]: 21341416 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38956395 bytes to primary EBWT file: CB_Testis_tp172/tmp/segment_juncs.1.bt2 Wrote 5335360 bytes to secondary EBWT file: CB_Testis_tp172/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21341416 bwtLen: 21341417 sz: 5335354 bwtSz: 5335355 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1333839 offsSz: 5335356 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 111154 numLines: 111154 ebwtTotLen: 7113856 ebwtTotSz: 7113856 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:19 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: 5335354 Using parameters --bmax 4001516 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4001516 --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 7; 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 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.04877e+06 (target: 4001515) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4001516) 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 3233508 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3233509 Getting block 2 of 7 Reserving size (4001516) 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 3617280 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3617281 Getting block 3 of 7 Reserving size (4001516) 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 2564535 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2564536 Getting block 4 of 7 Reserving size (4001516) 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 3891416 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3891417 Getting block 5 of 7 Reserving size (4001516) 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 1367159 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1367160 Getting block 6 of 7 Reserving size (4001516) 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 3387659 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3387660 Getting block 7 of 7 Reserving size (4001516) 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 3279853 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3279854 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5267774 fchr[G]: 10713618 fchr[T]: 15908292 fchr[$]: 21341416 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38956395 bytes to primary EBWT file: CB_Testis_tp172/tmp/segment_juncs.rev.1.bt2 Wrote 5335360 bytes to secondary EBWT file: CB_Testis_tp172/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21341416 bwtLen: 21341417 sz: 5335354 bwtSz: 5335355 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1333839 offsSz: 5335356 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 111154 numLines: 111154 ebwtTotLen: 7113856 ebwtTotSz: 7113856 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:18