Settings: Output files: "/scratch/9142573.1.p16/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/9142573.1.p16/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: 5324750 Using parameters --bmax 3993563 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3993563 --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: 3.04271e+06 (target: 3993562) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3993563) 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 2805995 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2805996 Getting block 2 of 7 Reserving size (3993563) 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 3161151 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3161152 Getting block 3 of 7 Reserving size (3993563) 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 3506750 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3506751 Getting block 4 of 7 Reserving size (3993563) 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 1824986 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1824987 Getting block 5 of 7 Reserving size (3993563) 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 3989080 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3989081 Getting block 6 of 7 Reserving size (3993563) 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 3208373 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3208374 Getting block 7 of 7 Reserving size (3993563) 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 2802659 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2802660 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5244887 fchr[G]: 10612642 fchr[T]: 15926265 fchr[$]: 21299000 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 40045340 bytes to primary EBWT file: /scratch/9142573.1.p16/tophat2/tmp/segment_juncs.1.bt2 Wrote 5324756 bytes to secondary EBWT file: /scratch/9142573.1.p16/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21299000 bwtLen: 21299001 sz: 5324750 bwtSz: 5324751 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1331188 offsSz: 5324752 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 110933 numLines: 110933 ebwtTotLen: 7099712 ebwtTotSz: 7099712 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:11 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: 5324750 Using parameters --bmax 3993563 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3993563 --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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; 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: 3.04271e+06 (target: 3993562) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3993563) 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 3154385 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3154386 Getting block 2 of 7 Reserving size (3993563) 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 2090500 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2090501 Getting block 3 of 7 Reserving size (3993563) 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 3541718 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3541719 Getting block 4 of 7 Reserving size (3993563) 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 2744365 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2744366 Getting block 5 of 7 Reserving size (3993563) 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 2380641 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2380642 Getting block 6 of 7 Reserving size (3993563) 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 3497632 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3497633 Getting block 7 of 7 Reserving size (3993563) 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 3889753 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3889754 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5244887 fchr[G]: 10612642 fchr[T]: 15926265 fchr[$]: 21299000 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 40045340 bytes to primary EBWT file: /scratch/9142573.1.p16/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 5324756 bytes to secondary EBWT file: /scratch/9142573.1.p16/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21299000 bwtLen: 21299001 sz: 5324750 bwtSz: 5324751 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1331188 offsSz: 5324752 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 110933 numLines: 110933 ebwtTotLen: 7099712 ebwtTotSz: 7099712 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:12