Settings: Output files: "CBKidneytp121/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: CBKidneytp121/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: 4056076 Using parameters --bmax 3042057 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3042057 --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: 2.31776e+06 (target: 3042056) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3042057) 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 2499382 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2499383 Getting block 2 of 7 Reserving size (3042057) 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 686494 (Using difference cover) Sorting block time: 00:00:01 Returning block of 686495 Getting block 3 of 7 Reserving size (3042057) 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 2899548 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2899549 Getting block 4 of 7 Reserving size (3042057) 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 2600708 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2600709 Getting block 5 of 7 Reserving size (3042057) 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 2500862 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2500863 Getting block 6 of 7 Reserving size (3042057) 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 2581315 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2581316 Getting block 7 of 7 Reserving size (3042057) 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 2455989 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2455990 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3898069 fchr[G]: 8074926 fchr[T]: 12154560 fchr[$]: 16224304 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30665768 bytes to primary EBWT file: CBKidneytp121/tmp/segment_juncs.1.bt2 Wrote 4056084 bytes to secondary EBWT file: CBKidneytp121/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16224304 bwtLen: 16224305 sz: 4056076 bwtSz: 4056077 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1014020 offsSz: 4056080 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 84502 numLines: 84502 ebwtTotLen: 5408128 ebwtTotSz: 5408128 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:13 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: 4056076 Using parameters --bmax 3042057 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3042057 --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: 00:00:01 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: 00:00:00 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 Avg bucket size: 2.02804e+06 (target: 3042056) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3042057) 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 1956633 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1956634 Getting block 2 of 8 Reserving size (3042057) 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 1563709 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1563710 Getting block 3 of 8 Reserving size (3042057) 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 1671250 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1671251 Getting block 4 of 8 Reserving size (3042057) 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 2674614 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2674615 Getting block 5 of 8 Reserving size (3042057) 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 3000301 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3000302 Getting block 6 of 8 Reserving size (3042057) 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 1537644 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1537645 Getting block 7 of 8 Reserving size (3042057) 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 2034745 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2034746 Getting block 8 of 8 Reserving size (3042057) 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 1785401 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1785402 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3898069 fchr[G]: 8074926 fchr[T]: 12154560 fchr[$]: 16224304 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30665768 bytes to primary EBWT file: CBKidneytp121/tmp/segment_juncs.rev.1.bt2 Wrote 4056084 bytes to secondary EBWT file: CBKidneytp121/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16224304 bwtLen: 16224305 sz: 4056076 bwtSz: 4056077 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1014020 offsSz: 4056080 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 84502 numLines: 84502 ebwtTotLen: 5408128 ebwtTotSz: 5408128 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17