Settings: Output files: "IR_Kidney_131/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_131/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: 3699641 Using parameters --bmax 2774731 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2774731 --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 Avg bucket size: 2.11408e+06 (target: 2774730) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2774731) 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 1804468 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1804469 Getting block 2 of 7 Reserving size (2774731) 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 1673035 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1673036 Getting block 3 of 7 Reserving size (2774731) 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 2069643 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2069644 Getting block 4 of 7 Reserving size (2774731) 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 2507951 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2507952 Getting block 5 of 7 Reserving size (2774731) 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 1677455 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1677456 Getting block 6 of 7 Reserving size (2774731) 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 2405355 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2405356 Getting block 7 of 7 Reserving size (2774731) 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 2660654 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2660655 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3577797 fchr[G]: 7426748 fchr[T]: 11076286 fchr[$]: 14798567 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 28327799 bytes to primary EBWT file: IR_Kidney_131/tmp/segment_juncs.1.bt2 Wrote 3699648 bytes to secondary EBWT file: IR_Kidney_131/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 14798567 bwtLen: 14798568 sz: 3699642 bwtSz: 3699642 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 924911 offsSz: 3699644 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 77076 numLines: 77076 ebwtTotLen: 4932864 ebwtTotSz: 4932864 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:09 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: 3699641 Using parameters --bmax 2774731 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2774731 --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 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... 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: 2.11408e+06 (target: 2774730) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2774731) 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 2575647 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2575648 Getting block 2 of 7 Reserving size (2774731) 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 2691013 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2691014 Getting block 3 of 7 Reserving size (2774731) 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 2552576 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2552577 Getting block 4 of 7 Reserving size (2774731) 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 1644303 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1644304 Getting block 5 of 7 Reserving size (2774731) 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 1871634 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1871635 Getting block 6 of 7 Reserving size (2774731) 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 2327646 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2327647 Getting block 7 of 7 Reserving size (2774731) 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 1135742 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1135743 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3577797 fchr[G]: 7426748 fchr[T]: 11076286 fchr[$]: 14798567 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 28327799 bytes to primary EBWT file: IR_Kidney_131/tmp/segment_juncs.rev.1.bt2 Wrote 3699648 bytes to secondary EBWT file: IR_Kidney_131/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 14798567 bwtLen: 14798568 sz: 3699642 bwtSz: 3699642 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 924911 offsSz: 3699644 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 77076 numLines: 77076 ebwtTotLen: 4932864 ebwtTotSz: 4932864 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:12