Settings: Output files: "MC_Testis_18b/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: MC_Testis_18b/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: 6532119 Using parameters --bmax 4899090 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4899090 --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 5; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.90316e+06 (target: 4899089) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (4899090) 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 4153144 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4153145 Getting block 2 of 9 Reserving size (4899090) 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 1504461 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1504462 Getting block 3 of 9 Reserving size (4899090) 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 3640649 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3640650 Getting block 4 of 9 Reserving size (4899090) 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 1982677 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1982678 Getting block 5 of 9 Reserving size (4899090) 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 3245840 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3245841 Getting block 6 of 9 Reserving size (4899090) 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 3634623 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3634624 Getting block 7 of 9 Reserving size (4899090) 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 2573865 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2573866 Getting block 8 of 9 Reserving size (4899090) 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 3808942 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3808943 Getting block 9 of 9 Reserving size (4899090) 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 1584267 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1584268 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6433017 fchr[G]: 13075585 fchr[T]: 19477803 fchr[$]: 26128476 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 46766033 bytes to primary EBWT file: MC_Testis_18b/tmp/segment_juncs.1.bt2 Wrote 6532124 bytes to secondary EBWT file: MC_Testis_18b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 26128476 bwtLen: 26128477 sz: 6532119 bwtSz: 6532120 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1633030 offsSz: 6532120 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 136086 numLines: 136086 ebwtTotLen: 8709504 ebwtTotSz: 8709504 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:21 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: 6532119 Using parameters --bmax 4899090 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4899090 --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: 00:00:02 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: 00:00:01 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: 3.73264e+06 (target: 4899089) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4899090) 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 3943160 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3943161 Getting block 2 of 7 Reserving size (4899090) 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 4571212 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4571213 Getting block 3 of 7 Reserving size (4899090) 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 4302596 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4302597 Getting block 4 of 7 Reserving size (4899090) 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 3456254 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3456255 Getting block 5 of 7 Reserving size (4899090) 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 4232233 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4232234 Getting block 6 of 7 Reserving size (4899090) 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 4789868 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4789869 Getting block 7 of 7 Reserving size (4899090) 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 833147 (Using difference cover) Sorting block time: 00:00:00 Returning block of 833148 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6433017 fchr[G]: 13075585 fchr[T]: 19477803 fchr[$]: 26128476 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 46766033 bytes to primary EBWT file: MC_Testis_18b/tmp/segment_juncs.rev.1.bt2 Wrote 6532124 bytes to secondary EBWT file: MC_Testis_18b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 26128476 bwtLen: 26128477 sz: 6532119 bwtSz: 6532120 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1633030 offsSz: 6532120 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 136086 numLines: 136086 ebwtTotLen: 8709504 ebwtTotSz: 8709504 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:21