Settings: Output files: "6M-HS/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: 6M-HS/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: 2987204 Using parameters --bmax 2240403 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2240403 --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 3, 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 Avg bucket size: 1.4936e+06 (target: 2240402) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2240403) 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 1584456 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1584457 Getting block 2 of 8 Reserving size (2240403) 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 1303933 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1303934 Getting block 3 of 8 Reserving size (2240403) 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 1241100 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1241101 Getting block 4 of 8 Reserving size (2240403) 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 1087345 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1087346 Getting block 5 of 8 Reserving size (2240403) 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 1388382 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1388383 Getting block 6 of 8 Reserving size (2240403) 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 2124120 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2124121 Getting block 7 of 8 Reserving size (2240403) 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 1558509 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1558510 Getting block 8 of 8 Reserving size (2240403) 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 1660967 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1660968 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3434374 fchr[G]: 5980978 fchr[T]: 8431905 fchr[$]: 11948819 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22872627 bytes to primary EBWT file: 6M-HS/tmp/segment_juncs.1.bt2 Wrote 2987212 bytes to secondary EBWT file: 6M-HS/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11948819 bwtLen: 11948820 sz: 2987205 bwtSz: 2987205 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 746802 offsSz: 2987208 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 62234 numLines: 62234 ebwtTotLen: 3982976 ebwtTotSz: 3982976 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:11 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: 2987204 Using parameters --bmax 2240403 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2240403 --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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.4936e+06 (target: 2240402) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2240403) 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 1957760 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1957761 Getting block 2 of 8 Reserving size (2240403) 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 2159678 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2159679 Getting block 3 of 8 Reserving size (2240403) 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 813545 (Using difference cover) Sorting block time: 00:00:01 Returning block of 813546 Getting block 4 of 8 Reserving size (2240403) 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 1979830 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1979831 Getting block 5 of 8 Reserving size (2240403) 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 587214 (Using difference cover) Sorting block time: 00:00:00 Returning block of 587215 Getting block 6 of 8 Reserving size (2240403) 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 1823126 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1823127 Getting block 7 of 8 Reserving size (2240403) 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 2112737 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2112738 Getting block 8 of 8 Reserving size (2240403) 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 514922 (Using difference cover) Sorting block time: 00:00:00 Returning block of 514923 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3434374 fchr[G]: 5980978 fchr[T]: 8431905 fchr[$]: 11948819 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22872627 bytes to primary EBWT file: 6M-HS/tmp/segment_juncs.rev.1.bt2 Wrote 2987212 bytes to secondary EBWT file: 6M-HS/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11948819 bwtLen: 11948820 sz: 2987205 bwtSz: 2987205 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 746802 offsSz: 2987208 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 62234 numLines: 62234 ebwtTotLen: 3982976 ebwtTotSz: 3982976 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:11