Settings: Output files: "/scratch/9142572.1.linga/tophat2/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: /scratch/9142572.1.linga/tophat2/tmp/segment_juncs.fa 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 bmax according to bmaxDivN setting: 5470300 Using parameters --bmax 4102725 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4102725 --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 1, merged 5; 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: 2.73515e+06 (target: 4102724) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4102725) 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 1759014 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1759015 Getting block 2 of 8 Reserving size (4102725) 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 3138223 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3138224 Getting block 3 of 8 Reserving size (4102725) 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 1158946 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1158947 Getting block 4 of 8 Reserving size (4102725) 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 3507592 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3507593 Getting block 5 of 8 Reserving size (4102725) 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 2123521 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2123522 Getting block 6 of 8 Reserving size (4102725) 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 3149215 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3149216 Getting block 7 of 8 Reserving size (4102725) 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 3867003 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3867004 Getting block 8 of 8 Reserving size (4102725) 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 3177679 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3177680 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5396847 fchr[G]: 10906410 fchr[T]: 16350433 fchr[$]: 21881200 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 41018322 bytes to primary EBWT file: /scratch/9142572.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 5470308 bytes to secondary EBWT file: /scratch/9142572.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21881200 bwtLen: 21881201 sz: 5470300 bwtSz: 5470301 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1367576 offsSz: 5470304 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 113965 numLines: 113965 ebwtTotLen: 7293760 ebwtTotSz: 7293760 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:16 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: 00:00:01 bmax according to bmaxDivN setting: 5470300 Using parameters --bmax 4102725 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4102725 --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 2, merged 8; 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: 3.12588e+06 (target: 4102724) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4102725) 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 3695941 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3695942 Getting block 2 of 7 Reserving size (4102725) 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 3607700 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3607701 Getting block 3 of 7 Reserving size (4102725) 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 3715579 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3715580 Getting block 4 of 7 Reserving size (4102725) 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 3688908 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3688909 Getting block 5 of 7 Reserving size (4102725) 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 1763485 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1763486 Getting block 6 of 7 Reserving size (4102725) 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 3507712 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3507713 Getting block 7 of 7 Reserving size (4102725) 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 1901869 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1901870 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5396847 fchr[G]: 10906410 fchr[T]: 16350433 fchr[$]: 21881200 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 41018322 bytes to primary EBWT file: /scratch/9142572.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 5470308 bytes to secondary EBWT file: /scratch/9142572.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21881200 bwtLen: 21881201 sz: 5470300 bwtSz: 5470301 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1367576 offsSz: 5470304 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 113965 numLines: 113965 ebwtTotLen: 7293760 ebwtTotSz: 7293760 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:14