Settings: Output files: "A8DE_13066_ATTCCT/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: A8DE_13066_ATTCCT/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:03 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:05 bmax according to bmaxDivN setting: 49316117 Using parameters --bmax 36987088 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 36987088 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:05 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: 00:00:01 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: 00:00:08 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: 00:00:06 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: 00:00:06 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.81806e+07 (target: 36987087) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (36987088) 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: 00:00:02 Sorting block of length 32128005 (Using difference cover) Sorting block time: 00:00:15 Returning block of 32128006 Getting block 2 of 7 Reserving size (36987088) 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: 00:00:02 Sorting block of length 27790240 (Using difference cover) Sorting block time: 00:00:15 Returning block of 27790241 Getting block 3 of 7 Reserving size (36987088) 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: 00:00:02 Sorting block of length 22265386 (Using difference cover) Sorting block time: 00:00:14 Returning block of 22265387 Getting block 4 of 7 Reserving size (36987088) 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: 00:00:02 Sorting block of length 34826091 (Using difference cover) Sorting block time: 00:00:20 Returning block of 34826092 Getting block 5 of 7 Reserving size (36987088) 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: 00:00:03 Sorting block of length 16516865 (Using difference cover) Sorting block time: 00:00:11 Returning block of 16516866 Getting block 6 of 7 Reserving size (36987088) 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: 00:00:02 Sorting block of length 33008743 (Using difference cover) Sorting block time: 00:00:23 Returning block of 33008744 Getting block 7 of 7 Reserving size (36987088) 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: 00:00:02 Sorting block of length 30729132 (Using difference cover) Sorting block time: 00:00:17 Returning block of 30729133 Exited Ebwt loop fchr[A]: 0 fchr[C]: 59918247 fchr[G]: 99093454 fchr[T]: 138299270 fchr[$]: 197264468 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 324416100 bytes to primary EBWT file: A8DE_13066_ATTCCT/tmp/segment_juncs.1.bt2 Wrote 49316124 bytes to secondary EBWT file: A8DE_13066_ATTCCT/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 197264468 bwtLen: 197264469 sz: 49316117 bwtSz: 49316118 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12329030 offsSz: 49316120 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 1027420 numLines: 1027420 ebwtTotLen: 65754880 ebwtTotSz: 65754880 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:03:08 Reading reference sizes Time reading reference sizes: 00:00:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 49316117 Using parameters --bmax 36987088 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 36987088 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:04 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: 00:00:02 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: 00:00:07 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.28774e+07 (target: 36987087) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (36987088) 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: 00:00:02 Sorting block of length 34082391 (Using difference cover) Sorting block time: 00:00:17 Returning block of 34082392 Getting block 2 of 6 Reserving size (36987088) 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: 00:00:03 Sorting block of length 35854992 (Using difference cover) Sorting block time: 00:00:20 Returning block of 35854993 Getting block 3 of 6 Reserving size (36987088) 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: 00:00:02 Sorting block of length 27346621 (Using difference cover) Sorting block time: 00:00:16 Returning block of 27346622 Getting block 4 of 6 Reserving size (36987088) 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: 00:00:03 Sorting block of length 32397243 (Using difference cover) Sorting block time: 00:00:18 Returning block of 32397244 Getting block 5 of 6 Reserving size (36987088) 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: 00:00:03 Sorting block of length 36574256 (Using difference cover) Sorting block time: 00:00:26 Returning block of 36574257 Getting block 6 of 6 Reserving size (36987088) 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: 00:00:02 Sorting block of length 31008960 (Using difference cover) Sorting block time: 00:00:19 Returning block of 31008961 Exited Ebwt loop fchr[A]: 0 fchr[C]: 59918247 fchr[G]: 99093454 fchr[T]: 138299270 fchr[$]: 197264468 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 324416100 bytes to primary EBWT file: A8DE_13066_ATTCCT/tmp/segment_juncs.rev.1.bt2 Wrote 49316124 bytes to secondary EBWT file: A8DE_13066_ATTCCT/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 197264468 bwtLen: 197264469 sz: 49316117 bwtSz: 49316118 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12329030 offsSz: 49316120 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 1027420 numLines: 1027420 ebwtTotLen: 65754880 ebwtTotSz: 65754880 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:02:52