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: 00:00:00 bmax according to bmaxDivN setting: 3286270 Using parameters --bmax 2464703 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2464703 --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: 00:00:01 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: 00:00:00 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 1; iterating... 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 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: 1.87787e+06 (target: 2464702) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2464703) 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 2374585 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2374586 Getting block 2 of 7 Reserving size (2464703) 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 1553981 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1553982 Getting block 3 of 7 Reserving size (2464703) 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 2026910 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2026911 Getting block 4 of 7 Reserving size (2464703) 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 1061371 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1061372 Getting block 5 of 7 Reserving size (2464703) 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 2178944 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2178945 Getting block 6 of 7 Reserving size (2464703) 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 2099058 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2099059 Getting block 7 of 7 Reserving size (2464703) 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 1850228 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1850229 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3779087 fchr[G]: 6603118 fchr[T]: 9356352 fchr[$]: 13145083 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 28608246 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.1.bt2 Wrote 3286276 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: 13145083 bwtLen: 13145084 sz: 3286271 bwtSz: 3286271 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 821568 offsSz: 3286272 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 68464 numLines: 68464 ebwtTotLen: 4381696 ebwtTotSz: 4381696 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:09 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: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 3286270 Using parameters --bmax 2464703 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2464703 --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 Avg bucket size: 1.64313e+06 (target: 2464702) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2464703) 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 2006052 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2006053 Getting block 2 of 8 Reserving size (2464703) 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 1859205 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1859206 Getting block 3 of 8 Reserving size (2464703) 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 1529486 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1529487 Getting block 4 of 8 Reserving size (2464703) 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 1180685 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1180686 Getting block 5 of 8 Reserving size (2464703) 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 2366710 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2366711 Getting block 6 of 8 Reserving size (2464703) 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 1343618 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1343619 Getting block 7 of 8 Reserving size (2464703) 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 1125798 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1125799 Getting block 8 of 8 Reserving size (2464703) 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 1733522 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1733523 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3779087 fchr[G]: 6603118 fchr[T]: 9356352 fchr[$]: 13145083 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 28608246 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.rev.1.bt2 Wrote 3286276 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: 13145083 bwtLen: 13145084 sz: 3286271 bwtSz: 3286271 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 821568 offsSz: 3286272 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 68464 numLines: 68464 ebwtTotLen: 4381696 ebwtTotSz: 4381696 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:07