Settings: Output files: "CBKidneytp172/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: CBKidneytp172/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: 3773739 Using parameters --bmax 2830305 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2830305 --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 Avg bucket size: 2.15642e+06 (target: 2830304) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2830305) 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 2449048 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2449049 Getting block 2 of 7 Reserving size (2830305) 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 1523402 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1523403 Getting block 3 of 7 Reserving size (2830305) 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 2454271 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2454272 Getting block 4 of 7 Reserving size (2830305) 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 2382124 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2382125 Getting block 5 of 7 Reserving size (2830305) 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 676586 (Using difference cover) Sorting block time: 00:00:00 Returning block of 676587 Getting block 6 of 7 Reserving size (2830305) 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 2809943 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2809944 Getting block 7 of 7 Reserving size (2830305) 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 2799576 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2799577 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3652951 fchr[G]: 7581283 fchr[T]: 11299334 fchr[$]: 15094956 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 28818362 bytes to primary EBWT file: CBKidneytp172/tmp/segment_juncs.1.bt2 Wrote 3773744 bytes to secondary EBWT file: CBKidneytp172/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15094956 bwtLen: 15094957 sz: 3773739 bwtSz: 3773740 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 943435 offsSz: 3773740 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 78620 numLines: 78620 ebwtTotLen: 5031680 ebwtTotSz: 5031680 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:10 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: 3773739 Using parameters --bmax 2830305 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2830305 --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 Avg bucket size: 1.67722e+06 (target: 2830304) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2830305) 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 2079680 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2079681 Getting block 2 of 9 Reserving size (2830305) 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 1683152 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1683153 Getting block 3 of 9 Reserving size (2830305) 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 1635313 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1635314 Getting block 4 of 9 Reserving size (2830305) 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 1451551 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1451552 Getting block 5 of 9 Reserving size (2830305) 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 1917694 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1917695 Getting block 6 of 9 Reserving size (2830305) 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 1356344 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1356345 Getting block 7 of 9 Reserving size (2830305) 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 2070532 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2070533 Getting block 8 of 9 Reserving size (2830305) 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 2356975 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2356976 Getting block 9 of 9 Reserving size (2830305) 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 543707 (Using difference cover) Sorting block time: 00:00:00 Returning block of 543708 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3652951 fchr[G]: 7581283 fchr[T]: 11299334 fchr[$]: 15094956 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 28818362 bytes to primary EBWT file: CBKidneytp172/tmp/segment_juncs.rev.1.bt2 Wrote 3773744 bytes to secondary EBWT file: CBKidneytp172/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15094956 bwtLen: 15094957 sz: 3773739 bwtSz: 3773740 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 943435 offsSz: 3773740 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 78620 numLines: 78620 ebwtTotLen: 5031680 ebwtTotSz: 5031680 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:12