Settings: Output files: "/scratch/8793165.1.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/8793165.1.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: 2661575 Using parameters --bmax 1996182 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1996182 --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: 00:00:00 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: 00:00:00 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 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: 1.5209e+06 (target: 1996181) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1996182) 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 1612832 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1612833 Getting block 2 of 7 Reserving size (1996182) 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 1871633 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1871634 Getting block 3 of 7 Reserving size (1996182) 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 1678149 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1678150 Getting block 4 of 7 Reserving size (1996182) 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 1318222 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1318223 Getting block 5 of 7 Reserving size (1996182) 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 1178442 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1178443 Getting block 6 of 7 Reserving size (1996182) 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 1815966 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1815967 Getting block 7 of 7 Reserving size (1996182) 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 1171050 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1171051 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2653220 fchr[G]: 5313069 fchr[T]: 7974280 fchr[$]: 10646300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22100569 bytes to primary EBWT file: /scratch/8793165.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2661580 bytes to secondary EBWT file: /scratch/8793165.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10646300 bwtLen: 10646301 sz: 2661575 bwtSz: 2661576 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 665394 offsSz: 2661576 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 55450 numLines: 55450 ebwtTotLen: 3548800 ebwtTotSz: 3548800 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:10 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: 00:00:00 bmax according to bmaxDivN setting: 2661575 Using parameters --bmax 1996182 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1996182 --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 6; 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: 1.5209e+06 (target: 1996181) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1996182) 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 696951 (Using difference cover) Sorting block time: 00:00:00 Returning block of 696952 Getting block 2 of 7 Reserving size (1996182) 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 1982968 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1982969 Getting block 3 of 7 Reserving size (1996182) 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 1612918 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1612919 Getting block 4 of 7 Reserving size (1996182) 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 1215079 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1215080 Getting block 5 of 7 Reserving size (1996182) 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 1475251 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1475252 Getting block 6 of 7 Reserving size (1996182) 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 1739902 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1739903 Getting block 7 of 7 Reserving size (1996182) 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 1923225 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1923226 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2653220 fchr[G]: 5313069 fchr[T]: 7974280 fchr[$]: 10646300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22100569 bytes to primary EBWT file: /scratch/8793165.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2661580 bytes to secondary EBWT file: /scratch/8793165.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10646300 bwtLen: 10646301 sz: 2661575 bwtSz: 2661576 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 665394 offsSz: 2661576 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 55450 numLines: 55450 ebwtTotLen: 3548800 ebwtTotSz: 3548800 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:08