Settings: Output files: "IR_Kidney_05F1C1/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: IR_Kidney_05F1C1/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: 3962829 Using parameters --bmax 2972122 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2972122 --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 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 Avg bucket size: 1.98141e+06 (target: 2972121) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2972122) 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 2893836 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2893837 Getting block 2 of 8 Reserving size (2972122) 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 1662743 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1662744 Getting block 3 of 8 Reserving size (2972122) 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 2453410 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2453411 Getting block 4 of 8 Reserving size (2972122) 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 2646039 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2646040 Getting block 5 of 8 Reserving size (2972122) 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 726344 (Using difference cover) Sorting block time: 00:00:00 Returning block of 726345 Getting block 6 of 8 Reserving size (2972122) 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 2489942 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2489943 Getting block 7 of 8 Reserving size (2972122) 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 731873 (Using difference cover) Sorting block time: 00:00:00 Returning block of 731874 Getting block 8 of 8 Reserving size (2972122) 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 2247122 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2247123 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3798880 fchr[G]: 7956143 fchr[T]: 11877064 fchr[$]: 15851316 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30034053 bytes to primary EBWT file: IR_Kidney_05F1C1/tmp/segment_juncs.1.bt2 Wrote 3962836 bytes to secondary EBWT file: IR_Kidney_05F1C1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15851316 bwtLen: 15851317 sz: 3962829 bwtSz: 3962830 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 990708 offsSz: 3962832 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 82559 numLines: 82559 ebwtTotLen: 5283776 ebwtTotSz: 5283776 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:12 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: 3962829 Using parameters --bmax 2972122 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2972122 --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 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 1; 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: 2.64189e+06 (target: 2972121) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (2972122) 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 2339222 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2339223 Getting block 2 of 6 Reserving size (2972122) 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 1980929 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1980930 Getting block 3 of 6 Reserving size (2972122) 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 2786153 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2786154 Getting block 4 of 6 Reserving size (2972122) 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 2911169 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2911170 Getting block 5 of 6 Reserving size (2972122) 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 2909340 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2909341 Getting block 6 of 6 Reserving size (2972122) 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 2924498 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2924499 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3798880 fchr[G]: 7956143 fchr[T]: 11877064 fchr[$]: 15851316 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30034053 bytes to primary EBWT file: IR_Kidney_05F1C1/tmp/segment_juncs.rev.1.bt2 Wrote 3962836 bytes to secondary EBWT file: IR_Kidney_05F1C1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15851316 bwtLen: 15851317 sz: 3962829 bwtSz: 3962830 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 990708 offsSz: 3962832 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 82559 numLines: 82559 ebwtTotLen: 5283776 ebwtTotSz: 5283776 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:11