Settings: Output files: "/scratch/8793045.1.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/8793045.1.linga/tophat2/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: 2532237 Using parameters --bmax 1899178 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1899178 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.26612e+06 (target: 1899177) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1899178) 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 615303 (Using difference cover) Sorting block time: 00:00:00 Returning block of 615304 Getting block 2 of 8 Reserving size (1899178) 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 1605344 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1605345 Getting block 3 of 8 Reserving size (1899178) 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 902787 (Using difference cover) Sorting block time: 00:00:00 Returning block of 902788 Getting block 4 of 8 Reserving size (1899178) 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 1533955 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1533956 Getting block 5 of 8 Reserving size (1899178) 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 1415308 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1415309 Getting block 6 of 8 Reserving size (1899178) 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 761505 (Using difference cover) Sorting block time: 00:00:00 Returning block of 761506 Getting block 7 of 8 Reserving size (1899178) 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 1575028 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1575029 Getting block 8 of 8 Reserving size (1899178) 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 1719713 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1719714 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2515404 fchr[G]: 5057436 fchr[T]: 7603696 fchr[$]: 10128950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21239842 bytes to primary EBWT file: /scratch/8793045.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2532244 bytes to secondary EBWT file: /scratch/8793045.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10128950 bwtLen: 10128951 sz: 2532238 bwtSz: 2532238 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 633060 offsSz: 2532240 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52755 numLines: 52755 ebwtTotLen: 3376320 ebwtTotSz: 3376320 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:08 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: 2532237 Using parameters --bmax 1899178 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1899178 --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: 1.68816e+06 (target: 1899177) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (1899178) 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 1868674 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1868675 Getting block 2 of 6 Reserving size (1899178) 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 1761122 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1761123 Getting block 3 of 6 Reserving size (1899178) 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 1804417 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1804418 Getting block 4 of 6 Reserving size (1899178) 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 1873609 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1873610 Getting block 5 of 6 Reserving size (1899178) 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 1416758 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1416759 Getting block 6 of 6 Reserving size (1899178) 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 1404365 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1404366 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2515404 fchr[G]: 5057436 fchr[T]: 7603696 fchr[$]: 10128950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21239842 bytes to primary EBWT file: /scratch/8793045.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2532244 bytes to secondary EBWT file: /scratch/8793045.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10128950 bwtLen: 10128951 sz: 2532238 bwtSz: 2532238 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 633060 offsSz: 2532240 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52755 numLines: 52755 ebwtTotLen: 3376320 ebwtTotSz: 3376320 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:08