Settings: Output files: "/scratch/9328371.1.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/9328371.1.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: 4145648 Using parameters --bmax 3109236 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3109236 --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 Split 2, 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 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.84251e+06 (target: 3109235) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (3109236) 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 694572 (Using difference cover) Sorting block time: 00:00:01 Returning block of 694573 Getting block 2 of 9 Reserving size (3109236) 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 2752672 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2752673 Getting block 3 of 9 Reserving size (3109236) 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 1438796 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1438797 Getting block 4 of 9 Reserving size (3109236) 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 2898976 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2898977 Getting block 5 of 9 Reserving size (3109236) 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 2159548 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2159549 Getting block 6 of 9 Reserving size (3109236) 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 2004424 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2004425 Getting block 7 of 9 Reserving size (3109236) 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 1483208 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1483209 Getting block 8 of 9 Reserving size (3109236) 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 3088372 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3088373 Getting block 9 of 9 Reserving size (3109236) 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 62017 (Using difference cover) Sorting block time: 00:00:00 Returning block of 62018 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4108566 fchr[G]: 8298347 fchr[T]: 12454051 fchr[$]: 16582593 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 31173498 bytes to primary EBWT file: /scratch/9328371.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 4145656 bytes to secondary EBWT file: /scratch/9328371.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16582593 bwtLen: 16582594 sz: 4145649 bwtSz: 4145649 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1036413 offsSz: 4145652 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 86368 numLines: 86368 ebwtTotLen: 5527552 ebwtTotSz: 5527552 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:22 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: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4145648 Using parameters --bmax 3109236 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3109236 --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 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: 2.07282e+06 (target: 3109235) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3109236) 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 2397150 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2397151 Getting block 2 of 8 Reserving size (3109236) 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 1784683 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1784684 Getting block 3 of 8 Reserving size (3109236) 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 2704896 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2704897 Getting block 4 of 8 Reserving size (3109236) 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 1732704 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1732705 Getting block 5 of 8 Reserving size (3109236) 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 2667007 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2667008 Getting block 6 of 8 Reserving size (3109236) 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 2040512 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2040513 Getting block 7 of 8 Reserving size (3109236) 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 2679768 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2679769 Getting block 8 of 8 Reserving size (3109236) 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 575866 (Using difference cover) Sorting block time: 00:00:01 Returning block of 575867 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4108566 fchr[G]: 8298347 fchr[T]: 12454051 fchr[$]: 16582593 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 31173498 bytes to primary EBWT file: /scratch/9328371.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 4145656 bytes to secondary EBWT file: /scratch/9328371.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16582593 bwtLen: 16582594 sz: 4145649 bwtSz: 4145649 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1036413 offsSz: 4145652 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 86368 numLines: 86368 ebwtTotLen: 5527552 ebwtTotSz: 5527552 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:23