Settings: Output files: "CB_Thyroid_tp81/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_Thyroid_tp81/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: 4296123 Using parameters --bmax 3222093 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3222093 --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 Split 1, merged 2; 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 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Avg bucket size: 1.90939e+06 (target: 3222092) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (3222093) 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 2048040 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2048041 Getting block 2 of 9 Reserving size (3222093) 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 2925982 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2925983 Getting block 3 of 9 Reserving size (3222093) 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 595848 (Using difference cover) Sorting block time: 00:00:00 Returning block of 595849 Getting block 4 of 9 Reserving size (3222093) 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 430874 (Using difference cover) Sorting block time: 00:00:00 Returning block of 430875 Getting block 5 of 9 Reserving size (3222093) 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 3015388 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3015389 Getting block 6 of 9 Reserving size (3222093) 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 1598718 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1598719 Getting block 7 of 9 Reserving size (3222093) 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 2565413 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2565414 Getting block 8 of 9 Reserving size (3222093) 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 2183026 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2183027 Getting block 9 of 9 Reserving size (3222093) 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 1821195 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1821196 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4095779 fchr[G]: 8700176 fchr[T]: 12951684 fchr[$]: 17184492 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32215417 bytes to primary EBWT file: CB_Thyroid_tp81/tmp/segment_juncs.1.bt2 Wrote 4296128 bytes to secondary EBWT file: CB_Thyroid_tp81/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17184492 bwtLen: 17184493 sz: 4296123 bwtSz: 4296124 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1074031 offsSz: 4296124 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 89503 numLines: 89503 ebwtTotLen: 5728192 ebwtTotSz: 5728192 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:21 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 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 4296123 Using parameters --bmax 3222093 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3222093 --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 1, 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 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: 2.14806e+06 (target: 3222092) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3222093) 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 3064396 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3064397 Getting block 2 of 8 Reserving size (3222093) 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 2761061 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2761062 Getting block 3 of 8 Reserving size (3222093) 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 1184649 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1184650 Getting block 4 of 8 Reserving size (3222093) 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 2549246 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2549247 Getting block 5 of 8 Reserving size (3222093) 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 1544370 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1544371 Getting block 6 of 8 Reserving size (3222093) 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 2581252 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2581253 Getting block 7 of 8 Reserving size (3222093) 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 2633796 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2633797 Getting block 8 of 8 Reserving size (3222093) 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 865715 (Using difference cover) Sorting block time: 00:00:00 Returning block of 865716 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4095779 fchr[G]: 8700176 fchr[T]: 12951684 fchr[$]: 17184492 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32215417 bytes to primary EBWT file: CB_Thyroid_tp81/tmp/segment_juncs.rev.1.bt2 Wrote 4296128 bytes to secondary EBWT file: CB_Thyroid_tp81/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17184492 bwtLen: 17184493 sz: 4296123 bwtSz: 4296124 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1074031 offsSz: 4296124 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 89503 numLines: 89503 ebwtTotLen: 5728192 ebwtTotSz: 5728192 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17