Settings: Output files: "./tophat_out/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: ./tophat_out/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: 5301284 Using parameters --bmax 3975963 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3975963 --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: 00:00:01 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: 00:00:00 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 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: 3.0293e+06 (target: 3975962) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3975963) 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 2535206 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2535207 Getting block 2 of 7 Reserving size (3975963) 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 3409334 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3409335 Getting block 3 of 7 Reserving size (3975963) 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 3007283 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3007284 Getting block 4 of 7 Reserving size (3975963) 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 2975116 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2975117 Getting block 5 of 7 Reserving size (3975963) 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 3422314 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3422315 Getting block 6 of 7 Reserving size (3975963) 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 3884223 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3884224 Getting block 7 of 7 Reserving size (3975963) 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 1971655 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1971656 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6141979 fchr[G]: 10659057 fchr[T]: 15043642 fchr[$]: 21205137 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 43611834 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.1.bt2 Wrote 5301292 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21205137 bwtLen: 21205138 sz: 5301285 bwtSz: 5301285 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1325322 offsSz: 5301288 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 110444 numLines: 110444 ebwtTotLen: 7068416 ebwtTotSz: 7068416 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:17 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: 00:00:01 bmax according to bmaxDivN setting: 5301284 Using parameters --bmax 3975963 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3975963 --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 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: 3.0293e+06 (target: 3975962) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3975963) 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 3774031 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3774032 Getting block 2 of 7 Reserving size (3975963) 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 3620281 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3620282 Getting block 3 of 7 Reserving size (3975963) 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 1235463 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1235464 Getting block 4 of 7 Reserving size (3975963) 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 3906580 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3906581 Getting block 5 of 7 Reserving size (3975963) 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 2084834 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2084835 Getting block 6 of 7 Reserving size (3975963) 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 3358366 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3358367 Getting block 7 of 7 Reserving size (3975963) 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 3225576 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3225577 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6141979 fchr[G]: 10659057 fchr[T]: 15043642 fchr[$]: 21205137 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 43611834 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.rev.1.bt2 Wrote 5301292 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21205137 bwtLen: 21205138 sz: 5301285 bwtSz: 5301285 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1325322 offsSz: 5301288 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 110444 numLines: 110444 ebwtTotLen: 7068416 ebwtTotSz: 7068416 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:17