Settings: Output files: "IR_Brain_IR122/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_Brain_IR122/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: 4246410 Using parameters --bmax 3184808 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3184808 --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 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 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: 00:00:01 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: 2.1232e+06 (target: 3184807) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3184808) 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 1386688 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1386689 Getting block 2 of 8 Reserving size (3184808) 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 2254126 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2254127 Getting block 3 of 8 Reserving size (3184808) 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 1991853 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1991854 Getting block 4 of 8 Reserving size (3184808) 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 1600326 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1600327 Getting block 5 of 8 Reserving size (3184808) 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 3136894 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3136895 Getting block 6 of 8 Reserving size (3184808) 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 3092667 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3092668 Getting block 7 of 8 Reserving size (3184808) 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 926693 (Using difference cover) Sorting block time: 00:00:01 Returning block of 926694 Getting block 8 of 8 Reserving size (3184808) 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 2596389 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2596390 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4058610 fchr[G]: 8554714 fchr[T]: 12749420 fchr[$]: 16985643 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 31884364 bytes to primary EBWT file: IR_Brain_IR122/tmp/segment_juncs.1.bt2 Wrote 4246416 bytes to secondary EBWT file: IR_Brain_IR122/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16985643 bwtLen: 16985644 sz: 4246411 bwtSz: 4246411 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1061603 offsSz: 4246412 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 88467 numLines: 88467 ebwtTotLen: 5661888 ebwtTotSz: 5661888 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:14 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4246410 Using parameters --bmax 3184808 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3184808 --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 1, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.42652e+06 (target: 3184807) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3184808) 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 2781213 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2781214 Getting block 2 of 7 Reserving size (3184808) 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 2749838 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2749839 Getting block 3 of 7 Reserving size (3184808) 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 2765433 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2765434 Getting block 4 of 7 Reserving size (3184808) 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 1994491 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1994492 Getting block 5 of 7 Reserving size (3184808) 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 2380894 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2380895 Getting block 6 of 7 Reserving size (3184808) 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 2684186 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2684187 Getting block 7 of 7 Reserving size (3184808) 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 1629582 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1629583 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4058610 fchr[G]: 8554714 fchr[T]: 12749420 fchr[$]: 16985643 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 31884364 bytes to primary EBWT file: IR_Brain_IR122/tmp/segment_juncs.rev.1.bt2 Wrote 4246416 bytes to secondary EBWT file: IR_Brain_IR122/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16985643 bwtLen: 16985644 sz: 4246411 bwtSz: 4246411 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1061603 offsSz: 4246412 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 88467 numLines: 88467 ebwtTotLen: 5661888 ebwtTotSz: 5661888 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:13