Settings: Output files: "/scratch/8793406.1.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/8793406.1.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: 00:00:00 bmax according to bmaxDivN setting: 2568775 Using parameters --bmax 1926582 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1926582 --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 7; 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: 1.46787e+06 (target: 1926581) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1926582) 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 1874113 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1874114 Getting block 2 of 7 Reserving size (1926582) 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 1885803 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1885804 Getting block 3 of 7 Reserving size (1926582) 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 904458 (Using difference cover) Sorting block time: 00:00:00 Returning block of 904459 Getting block 4 of 7 Reserving size (1926582) 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 1361727 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1361728 Getting block 5 of 7 Reserving size (1926582) 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 1488374 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1488375 Getting block 6 of 7 Reserving size (1926582) 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 1690285 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1690286 Getting block 7 of 7 Reserving size (1926582) 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 1070334 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1070335 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2539538 fchr[G]: 5143594 fchr[T]: 7723597 fchr[$]: 10275100 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21492995 bytes to primary EBWT file: /scratch/8793406.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2568780 bytes to secondary EBWT file: /scratch/8793406.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10275100 bwtLen: 10275101 sz: 2568775 bwtSz: 2568776 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 642194 offsSz: 2568776 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 53517 numLines: 53517 ebwtTotLen: 3425088 ebwtTotSz: 3425088 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: 2568775 Using parameters --bmax 1926582 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1926582 --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: 1.46787e+06 (target: 1926581) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1926582) 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 1195875 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1195876 Getting block 2 of 7 Reserving size (1926582) 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 1771913 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1771914 Getting block 3 of 7 Reserving size (1926582) 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 1925615 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1925616 Getting block 4 of 7 Reserving size (1926582) 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 1880338 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1880339 Getting block 5 of 7 Reserving size (1926582) 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 855523 (Using difference cover) Sorting block time: 00:00:00 Returning block of 855524 Getting block 6 of 7 Reserving size (1926582) 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 1901674 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1901675 Getting block 7 of 7 Reserving size (1926582) 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 744156 (Using difference cover) Sorting block time: 00:00:01 Returning block of 744157 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2539538 fchr[G]: 5143594 fchr[T]: 7723597 fchr[$]: 10275100 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21492995 bytes to primary EBWT file: /scratch/8793406.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2568780 bytes to secondary EBWT file: /scratch/8793406.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10275100 bwtLen: 10275101 sz: 2568775 bwtSz: 2568776 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 642194 offsSz: 2568776 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 53517 numLines: 53517 ebwtTotLen: 3425088 ebwtTotSz: 3425088 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:08