Settings: Output files: "CB_Spleen_tp121/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_Spleen_tp121/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: 5174245 Using parameters --bmax 3880684 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3880684 --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 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 2, 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 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 Avg bucket size: 2.58712e+06 (target: 3880683) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3880684) 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 2495278 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2495279 Getting block 2 of 8 Reserving size (3880684) 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 2039252 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2039253 Getting block 3 of 8 Reserving size (3880684) 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 2316151 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2316152 Getting block 4 of 8 Reserving size (3880684) 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 2855091 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2855092 Getting block 5 of 8 Reserving size (3880684) 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 3517956 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3517957 Getting block 6 of 8 Reserving size (3880684) 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 3516493 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3516494 Getting block 7 of 8 Reserving size (3880684) 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 883784 (Using difference cover) Sorting block time: 00:00:00 Returning block of 883785 Getting block 8 of 8 Reserving size (3880684) 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 3072971 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3072972 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4941429 fchr[G]: 10393120 fchr[T]: 15524143 fchr[$]: 20696983 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38085737 bytes to primary EBWT file: CB_Spleen_tp121/tmp/segment_juncs.1.bt2 Wrote 5174252 bytes to secondary EBWT file: CB_Spleen_tp121/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20696983 bwtLen: 20696984 sz: 5174246 bwtSz: 5174246 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1293562 offsSz: 5174248 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 107797 numLines: 107797 ebwtTotLen: 6899008 ebwtTotSz: 6899008 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:24 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: 00:00:00 bmax according to bmaxDivN setting: 5174245 Using parameters --bmax 3880684 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3880684 --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 3, 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 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 Avg bucket size: 2.58712e+06 (target: 3880683) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3880684) 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 1500395 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1500396 Getting block 2 of 8 Reserving size (3880684) 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 3196376 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3196377 Getting block 3 of 8 Reserving size (3880684) 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 2311771 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2311772 Getting block 4 of 8 Reserving size (3880684) 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 1623696 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1623697 Getting block 5 of 8 Reserving size (3880684) 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 3305845 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3305846 Getting block 6 of 8 Reserving size (3880684) 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 2170302 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2170303 Getting block 7 of 8 Reserving size (3880684) 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 3062359 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3062360 Getting block 8 of 8 Reserving size (3880684) 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 3526232 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3526233 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4941429 fchr[G]: 10393120 fchr[T]: 15524143 fchr[$]: 20696983 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 38085737 bytes to primary EBWT file: CB_Spleen_tp121/tmp/segment_juncs.rev.1.bt2 Wrote 5174252 bytes to secondary EBWT file: CB_Spleen_tp121/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20696983 bwtLen: 20696984 sz: 5174246 bwtSz: 5174246 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1293562 offsSz: 5174248 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 107797 numLines: 107797 ebwtTotLen: 6899008 ebwtTotSz: 6899008 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:20