Settings: Output files: "/scratch/8793224.1.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/8793224.1.linga/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: 2904212 Using parameters --bmax 2178159 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2178159 --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 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 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.45211e+06 (target: 2178158) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2178159) 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 1976756 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1976757 Getting block 2 of 8 Reserving size (2178159) 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 1656822 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1656823 Getting block 3 of 8 Reserving size (2178159) 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 1257033 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1257034 Getting block 4 of 8 Reserving size (2178159) 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 1545959 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1545960 Getting block 5 of 8 Reserving size (2178159) 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 1107404 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1107405 Getting block 6 of 8 Reserving size (2178159) 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 1855908 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1855909 Getting block 7 of 8 Reserving size (2178159) 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 797306 (Using difference cover) Sorting block time: 00:00:00 Returning block of 797307 Getting block 8 of 8 Reserving size (2178159) 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 1419655 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1419656 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2911924 fchr[G]: 5791633 fchr[T]: 8657024 fchr[$]: 11616850 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23721454 bytes to primary EBWT file: /scratch/8793224.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2904220 bytes to secondary EBWT file: /scratch/8793224.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11616850 bwtLen: 11616851 sz: 2904213 bwtSz: 2904213 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 726054 offsSz: 2904216 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 60505 numLines: 60505 ebwtTotLen: 3872320 ebwtTotSz: 3872320 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:13 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: 2904212 Using parameters --bmax 2178159 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2178159 --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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.65955e+06 (target: 2178158) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2178159) 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 1496573 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1496574 Getting block 2 of 7 Reserving size (2178159) 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 1952496 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1952497 Getting block 3 of 7 Reserving size (2178159) 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 545831 (Using difference cover) Sorting block time: 00:00:00 Returning block of 545832 Getting block 4 of 7 Reserving size (2178159) 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 1688600 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1688601 Getting block 5 of 7 Reserving size (2178159) 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 1783253 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1783254 Getting block 6 of 7 Reserving size (2178159) 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 2003053 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2003054 Getting block 7 of 7 Reserving size (2178159) 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 2147038 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2147039 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2911924 fchr[G]: 5791633 fchr[T]: 8657024 fchr[$]: 11616850 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23721454 bytes to primary EBWT file: /scratch/8793224.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2904220 bytes to secondary EBWT file: /scratch/8793224.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11616850 bwtLen: 11616851 sz: 2904213 bwtSz: 2904213 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 726054 offsSz: 2904216 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 60505 numLines: 60505 ebwtTotLen: 3872320 ebwtTotSz: 3872320 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:11