Settings: Output files: "CB_Spleen_tp4a/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: CB_Spleen_tp4a/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: 4836325 Using parameters --bmax 3627244 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3627244 --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 2, 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 Avg bucket size: 2.76361e+06 (target: 3627243) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3627244) 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 3601971 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3601972 Getting block 2 of 7 Reserving size (3627244) 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 2700156 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2700157 Getting block 3 of 7 Reserving size (3627244) 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 1261891 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1261892 Getting block 4 of 7 Reserving size (3627244) 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 2426559 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2426560 Getting block 5 of 7 Reserving size (3627244) 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 3153372 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3153373 Getting block 6 of 7 Reserving size (3627244) 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 2694562 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2694563 Getting block 7 of 7 Reserving size (3627244) 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 3506783 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3506784 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4608984 fchr[G]: 9808258 fchr[T]: 14547249 fchr[$]: 19345300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 35860259 bytes to primary EBWT file: CB_Spleen_tp4a/tmp/segment_juncs.1.bt2 Wrote 4836332 bytes to secondary EBWT file: CB_Spleen_tp4a/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19345300 bwtLen: 19345301 sz: 4836325 bwtSz: 4836326 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1209082 offsSz: 4836328 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 100757 numLines: 100757 ebwtTotLen: 6448448 ebwtTotSz: 6448448 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:18 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: 4836325 Using parameters --bmax 3627244 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3627244 --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: 2.41816e+06 (target: 3627243) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3627244) 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 1970433 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1970434 Getting block 2 of 8 Reserving size (3627244) 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 3345343 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3345344 Getting block 3 of 8 Reserving size (3627244) 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 2010187 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2010188 Getting block 4 of 8 Reserving size (3627244) 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 2034699 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2034700 Getting block 5 of 8 Reserving size (3627244) 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 3441590 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3441591 Getting block 6 of 8 Reserving size (3627244) 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 1738734 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1738735 Getting block 7 of 8 Reserving size (3627244) 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 3543291 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3543292 Getting block 8 of 8 Reserving size (3627244) 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 1261016 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1261017 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4608984 fchr[G]: 9808258 fchr[T]: 14547249 fchr[$]: 19345300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 35860259 bytes to primary EBWT file: CB_Spleen_tp4a/tmp/segment_juncs.rev.1.bt2 Wrote 4836332 bytes to secondary EBWT file: CB_Spleen_tp4a/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19345300 bwtLen: 19345301 sz: 4836325 bwtSz: 4836326 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1209082 offsSz: 4836328 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 100757 numLines: 100757 ebwtTotLen: 6448448 ebwtTotSz: 6448448 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:18