Settings: Output files: "CB_Thyroid_tp3a2/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_tp3a2/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: 4588232 Using parameters --bmax 3441174 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3441174 --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: 00:00:01 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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.29412e+06 (target: 3441173) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3441174) 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 1743295 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1743296 Getting block 2 of 8 Reserving size (3441174) 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 2337895 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2337896 Getting block 3 of 8 Reserving size (3441174) 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 1225899 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1225900 Getting block 4 of 8 Reserving size (3441174) 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 3011349 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3011350 Getting block 5 of 8 Reserving size (3441174) 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 3347403 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3347404 Getting block 6 of 8 Reserving size (3441174) 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 1860430 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1860431 Getting block 7 of 8 Reserving size (3441174) 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 2144835 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2144836 Getting block 8 of 8 Reserving size (3441174) 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 2681817 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2681818 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4367650 fchr[G]: 9283994 fchr[T]: 13841727 fchr[$]: 18352930 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 34108031 bytes to primary EBWT file: CB_Thyroid_tp3a2/tmp/segment_juncs.1.bt2 Wrote 4588240 bytes to secondary EBWT file: CB_Thyroid_tp3a2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18352930 bwtLen: 18352931 sz: 4588233 bwtSz: 4588233 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1147059 offsSz: 4588236 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 95589 numLines: 95589 ebwtTotLen: 6117696 ebwtTotSz: 6117696 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:18 Reading reference sizes Time reading reference sizes: 00:00:00 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: 4588232 Using parameters --bmax 3441174 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3441174 --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 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 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: 2.29412e+06 (target: 3441173) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3441174) 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 1801995 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1801996 Getting block 2 of 8 Reserving size (3441174) 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 2682564 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2682565 Getting block 3 of 8 Reserving size (3441174) 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 2974382 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2974383 Getting block 4 of 8 Reserving size (3441174) 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 2039973 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2039974 Getting block 5 of 8 Reserving size (3441174) 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 3063088 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3063089 Getting block 6 of 8 Reserving size (3441174) 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 835559 (Using difference cover) Sorting block time: 00:00:01 Returning block of 835560 Getting block 7 of 8 Reserving size (3441174) 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 3250005 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3250006 Getting block 8 of 8 Reserving size (3441174) 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 1705357 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1705358 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4367650 fchr[G]: 9283994 fchr[T]: 13841727 fchr[$]: 18352930 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 34108031 bytes to primary EBWT file: CB_Thyroid_tp3a2/tmp/segment_juncs.rev.1.bt2 Wrote 4588240 bytes to secondary EBWT file: CB_Thyroid_tp3a2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18352930 bwtLen: 18352931 sz: 4588233 bwtSz: 4588233 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1147059 offsSz: 4588236 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 95589 numLines: 95589 ebwtTotLen: 6117696 ebwtTotSz: 6117696 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:19