Settings: Output files: "/scratch/8792866.1.p8/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/8792866.1.p8/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: 2525912 Using parameters --bmax 1894434 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1894434 --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 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 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.68394e+06 (target: 1894433) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (1894434) 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 1793145 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1793146 Getting block 2 of 6 Reserving size (1894434) 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 1415638 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1415639 Getting block 3 of 6 Reserving size (1894434) 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 1761504 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1761505 Getting block 4 of 6 Reserving size (1894434) 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 1801274 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1801275 Getting block 5 of 6 Reserving size (1894434) 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 1523834 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1523835 Getting block 6 of 6 Reserving size (1894434) 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 1808250 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1808251 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2502878 fchr[G]: 5052892 fchr[T]: 7595614 fchr[$]: 10103650 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21200325 bytes to primary EBWT file: /scratch/8792866.1.p8/tophat2/tmp/segment_juncs.1.bt2 Wrote 2525920 bytes to secondary EBWT file: /scratch/8792866.1.p8/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10103650 bwtLen: 10103651 sz: 2525913 bwtSz: 2525913 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 631479 offsSz: 2525916 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52624 numLines: 52624 ebwtTotLen: 3367936 ebwtTotSz: 3367936 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:04 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: 2525912 Using parameters --bmax 1894434 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1894434 --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: 00:00:00 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: 00:00:00 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: 1.12263e+06 (target: 1894433) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (1894434) 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 658515 (Using difference cover) Sorting block time: 00:00:00 Returning block of 658516 Getting block 2 of 9 Reserving size (1894434) 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 1280243 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1280244 Getting block 3 of 9 Reserving size (1894434) 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 646822 (Using difference cover) Sorting block time: 00:00:00 Returning block of 646823 Getting block 4 of 9 Reserving size (1894434) 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 1502519 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1502520 Getting block 5 of 9 Reserving size (1894434) 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 1021750 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1021751 Getting block 6 of 9 Reserving size (1894434) 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 1132943 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1132944 Getting block 7 of 9 Reserving size (1894434) 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 1767596 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1767597 Getting block 8 of 9 Reserving size (1894434) 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 1414902 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1414903 Getting block 9 of 9 Reserving size (1894434) 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 678352 (Using difference cover) Sorting block time: 00:00:01 Returning block of 678353 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2502878 fchr[G]: 5052892 fchr[T]: 7595614 fchr[$]: 10103650 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21200325 bytes to primary EBWT file: /scratch/8792866.1.p8/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2525920 bytes to secondary EBWT file: /scratch/8792866.1.p8/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10103650 bwtLen: 10103651 sz: 2525913 bwtSz: 2525913 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 631479 offsSz: 2525916 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52624 numLines: 52624 ebwtTotLen: 3367936 ebwtTotSz: 3367936 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:05