Settings: Output files: "/scratch/8793036.1.p8/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/8793036.1.p8/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: 2730112 Using parameters --bmax 2047584 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2047584 --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: 00:00:00 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: 1.36506e+06 (target: 2047583) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2047584) 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 1539749 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1539750 Getting block 2 of 8 Reserving size (2047584) 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 822531 (Using difference cover) Sorting block time: 00:00:00 Returning block of 822532 Getting block 3 of 8 Reserving size (2047584) 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 1470572 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1470573 Getting block 4 of 8 Reserving size (2047584) 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 1192521 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1192522 Getting block 5 of 8 Reserving size (2047584) 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 1955282 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1955283 Getting block 6 of 8 Reserving size (2047584) 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 1694373 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1694374 Getting block 7 of 8 Reserving size (2047584) 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 1336045 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1336046 Getting block 8 of 8 Reserving size (2047584) 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 909370 (Using difference cover) Sorting block time: 00:00:00 Returning block of 909371 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2706477 fchr[G]: 5450148 fchr[T]: 8189653 fchr[$]: 10920450 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22573185 bytes to primary EBWT file: /scratch/8793036.1.p8/tophat2/tmp/segment_juncs.1.bt2 Wrote 2730120 bytes to secondary EBWT file: /scratch/8793036.1.p8/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10920450 bwtLen: 10920451 sz: 2730113 bwtSz: 2730113 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 682529 offsSz: 2730116 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 56878 numLines: 56878 ebwtTotLen: 3640192 ebwtTotSz: 3640192 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:05 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: 2730112 Using parameters --bmax 2047584 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2047584 --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: 00:00:00 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: 1.36506e+06 (target: 2047583) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2047584) 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 706066 (Using difference cover) Sorting block time: 00:00:00 Returning block of 706067 Getting block 2 of 8 Reserving size (2047584) 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 1839065 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1839066 Getting block 3 of 8 Reserving size (2047584) 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 1201519 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1201520 Getting block 4 of 8 Reserving size (2047584) 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 991898 (Using difference cover) Sorting block time: 00:00:00 Returning block of 991899 Getting block 5 of 8 Reserving size (2047584) 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 1708047 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1708048 Getting block 6 of 8 Reserving size (2047584) 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 1948401 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1948402 Getting block 7 of 8 Reserving size (2047584) 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 855477 (Using difference cover) Sorting block time: 00:00:01 Returning block of 855478 Getting block 8 of 8 Reserving size (2047584) 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 1669970 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1669971 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2706477 fchr[G]: 5450148 fchr[T]: 8189653 fchr[$]: 10920450 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22573185 bytes to primary EBWT file: /scratch/8793036.1.p8/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2730120 bytes to secondary EBWT file: /scratch/8793036.1.p8/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10920450 bwtLen: 10920451 sz: 2730113 bwtSz: 2730113 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 682529 offsSz: 2730116 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 56878 numLines: 56878 ebwtTotLen: 3640192 ebwtTotSz: 3640192 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:05