Settings: Output files: "/scratch/8793105.1.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/8793105.1.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: 2826750 Using parameters --bmax 2120063 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2120063 --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 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: 1.25633e+06 (target: 2120062) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2120063) 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 404933 (Using difference cover) Sorting block time: 00:00:00 Returning block of 404934 Getting block 2 of 9 Reserving size (2120063) 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 1918893 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1918894 Getting block 3 of 9 Reserving size (2120063) 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 940567 (Using difference cover) Sorting block time: 00:00:01 Returning block of 940568 Getting block 4 of 9 Reserving size (2120063) 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 1574211 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1574212 Getting block 5 of 9 Reserving size (2120063) 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 1266098 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1266099 Getting block 6 of 9 Reserving size (2120063) 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 1073771 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1073772 Getting block 7 of 9 Reserving size (2120063) 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 1939418 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1939419 Getting block 8 of 9 Reserving size (2120063) 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 1274697 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1274698 Getting block 9 of 9 Reserving size (2120063) 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 914404 (Using difference cover) Sorting block time: 00:00:01 Returning block of 914405 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2827691 fchr[G]: 5640059 fchr[T]: 8444980 fchr[$]: 11307000 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23212466 bytes to primary EBWT file: /scratch/8793105.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2826756 bytes to secondary EBWT file: /scratch/8793105.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11307000 bwtLen: 11307001 sz: 2826750 bwtSz: 2826751 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 706688 offsSz: 2826752 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58891 numLines: 58891 ebwtTotLen: 3769024 ebwtTotSz: 3769024 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:12 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: 2826750 Using parameters --bmax 2120063 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2120063 --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 Avg bucket size: 1.41337e+06 (target: 2120062) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2120063) 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 749910 (Using difference cover) Sorting block time: 00:00:00 Returning block of 749911 Getting block 2 of 8 Reserving size (2120063) 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 2009482 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2009483 Getting block 3 of 8 Reserving size (2120063) 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 2031939 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2031940 Getting block 4 of 8 Reserving size (2120063) 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 893042 (Using difference cover) Sorting block time: 00:00:00 Returning block of 893043 Getting block 5 of 8 Reserving size (2120063) 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 1789493 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1789494 Getting block 6 of 8 Reserving size (2120063) 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 593116 (Using difference cover) Sorting block time: 00:00:00 Returning block of 593117 Getting block 7 of 8 Reserving size (2120063) 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 1972624 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1972625 Getting block 8 of 8 Reserving size (2120063) 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 1267387 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1267388 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2827691 fchr[G]: 5640059 fchr[T]: 8444980 fchr[$]: 11307000 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23212466 bytes to primary EBWT file: /scratch/8793105.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2826756 bytes to secondary EBWT file: /scratch/8793105.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11307000 bwtLen: 11307001 sz: 2826750 bwtSz: 2826751 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 706688 offsSz: 2826752 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58891 numLines: 58891 ebwtTotLen: 3769024 ebwtTotSz: 3769024 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10