Settings: Output files: "MCMuscleE1b/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: MCMuscleE1b/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: 3281642 Using parameters --bmax 2461232 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2461232 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.87522e+06 (target: 2461231) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2461232) 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 2427474 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2427475 Getting block 2 of 7 Reserving size (2461232) 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 1039806 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1039807 Getting block 3 of 7 Reserving size (2461232) 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 2276458 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2276459 Getting block 4 of 7 Reserving size (2461232) 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 2357680 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2357681 Getting block 5 of 7 Reserving size (2461232) 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 2005184 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2005185 Getting block 6 of 7 Reserving size (2461232) 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 2234851 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2234852 Getting block 7 of 7 Reserving size (2461232) 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 785109 (Using difference cover) Sorting block time: 00:00:00 Returning block of 785110 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3194542 fchr[G]: 6601436 fchr[T]: 9867481 fchr[$]: 13126568 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 25579403 bytes to primary EBWT file: MCMuscleE1b/tmp/segment_juncs.1.bt2 Wrote 3281648 bytes to secondary EBWT file: MCMuscleE1b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 13126568 bwtLen: 13126569 sz: 3281642 bwtSz: 3281643 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 820411 offsSz: 3281644 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 68368 numLines: 68368 ebwtTotLen: 4375552 ebwtTotSz: 4375552 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:09 Reading reference sizes Time reading reference sizes: 00:00:01 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: 3281642 Using parameters --bmax 2461232 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2461232 --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 Avg bucket size: 1.64082e+06 (target: 2461231) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2461232) 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 2371671 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2371672 Getting block 2 of 8 Reserving size (2461232) 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 1518925 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1518926 Getting block 3 of 8 Reserving size (2461232) 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 1059942 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1059943 Getting block 4 of 8 Reserving size (2461232) 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 1488738 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1488739 Getting block 5 of 8 Reserving size (2461232) 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 1623776 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1623777 Getting block 6 of 8 Reserving size (2461232) 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 2427082 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2427083 Getting block 7 of 8 Reserving size (2461232) 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 1690774 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1690775 Getting block 8 of 8 Reserving size (2461232) 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 945653 (Using difference cover) Sorting block time: 00:00:01 Returning block of 945654 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3194542 fchr[G]: 6601436 fchr[T]: 9867481 fchr[$]: 13126568 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 25579403 bytes to primary EBWT file: MCMuscleE1b/tmp/segment_juncs.rev.1.bt2 Wrote 3281648 bytes to secondary EBWT file: MCMuscleE1b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 13126568 bwtLen: 13126569 sz: 3281642 bwtSz: 3281643 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 820411 offsSz: 3281644 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 68368 numLines: 68368 ebwtTotLen: 4375552 ebwtTotSz: 4375552 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:11