Settings: Output files: "/projects/NBL/HS1799/61074AAXX_5/tophat_wj/tmp/segment_juncs.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) 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: /projects/NBL/HS1799/61074AAXX_5/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:50 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:26 bmax according to bmaxDivN setting: 101964443 Using parameters --bmax 76473333 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 76473333 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:21 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:04 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:09 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: 00:00:33 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.09822e+07 (target: 76473332) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (76473333) 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: 00:00:08 Sorting block of length 29516684 (Using difference cover) Sorting block time: 00:00:25 Returning block of 29516685 Getting block 2 of 8 Reserving size (76473333) 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: 00:00:09 Sorting block of length 51175646 (Using difference cover) Sorting block time: 00:00:50 Returning block of 51175647 Getting block 3 of 8 Reserving size (76473333) 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: 00:00:11 Sorting block of length 51652438 (Using difference cover) Sorting block time: 00:00:49 Returning block of 51652439 Getting block 4 of 8 Reserving size (76473333) 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: 00:00:14 Sorting block of length 76084408 (Using difference cover) Sorting block time: 00:01:12 Returning block of 76084409 Getting block 5 of 8 Reserving size (76473333) 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: 00:00:14 Sorting block of length 59185027 (Using difference cover) Sorting block time: 00:00:57 Returning block of 59185028 Getting block 6 of 8 Reserving size (76473333) 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: 00:00:14 Sorting block of length 22798413 (Using difference cover) Sorting block time: 00:00:21 Returning block of 22798414 Getting block 7 of 8 Reserving size (76473333) 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: 00:00:15 Sorting block of length 62734671 (Using difference cover) Sorting block time: 00:00:57 Returning block of 62734672 Getting block 8 of 8 Reserving size (76473333) 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: 00:00:08 Sorting block of length 54710479 (Using difference cover) Sorting block time: 00:00:48 Returning block of 54710480 Exited Ebwt loop fchr[A]: 0 fchr[C]: 101107366 fchr[G]: 202697985 fchr[T]: 303411269 fchr[$]: 407857773 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 741255866 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_5/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 50982228 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_5/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 407857773 bwtLen: 407857774 sz: 101964444 bwtSz: 101964444 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12745556 offsSz: 50982224 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 910397 numSides: 1820794 numLines: 1820794 ebwtTotLen: 116530816 ebwtTotSz: 116530816 Total time for call to driver() for forward index: 00:11:29 Reading reference sizes Time reading reference sizes: 00:00:08 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:26 bmax according to bmaxDivN setting: 101964443 Using parameters --bmax 76473333 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 76473333 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:18 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:05 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:08 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: 00:00:33 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.09822e+07 (target: 76473332) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (76473333) 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: 00:00:08 Sorting block of length 23456217 (Using difference cover) Sorting block time: 00:00:18 Returning block of 23456218 Getting block 2 of 8 Reserving size (76473333) 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: 00:00:10 Sorting block of length 70052423 (Using difference cover) Sorting block time: 00:01:02 Returning block of 70052424 Getting block 3 of 8 Reserving size (76473333) 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: 00:00:11 Sorting block of length 41949744 (Using difference cover) Sorting block time: 00:00:37 Returning block of 41949745 Getting block 4 of 8 Reserving size (76473333) 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: 00:00:12 Sorting block of length 41863029 (Using difference cover) Sorting block time: 00:00:44 Returning block of 41863030 Getting block 5 of 8 Reserving size (76473333) 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: 00:00:14 Sorting block of length 72974313 (Using difference cover) Sorting block time: 00:01:13 Returning block of 72974314 Getting block 6 of 8 Reserving size (76473333) 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: 00:00:14 Sorting block of length 32841010 (Using difference cover) Sorting block time: 00:00:33 Returning block of 32841011 Getting block 7 of 8 Reserving size (76473333) 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: 00:00:15 Sorting block of length 73149339 (Using difference cover) Sorting block time: 00:01:10 Returning block of 73149340 Getting block 8 of 8 Reserving size (76473333) 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: 00:00:09 Sorting block of length 51571691 (Using difference cover) Sorting block time: 00:00:47 Returning block of 51571692 Exited Ebwt loop fchr[A]: 0 fchr[C]: 101107366 fchr[G]: 202697985 fchr[T]: 303411269 fchr[$]: 407857773 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 741255866 bytes to primary EBWT file: /projects/NBL/HS1799/61074AAXX_5/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 50982228 bytes to secondary EBWT file: /projects/NBL/HS1799/61074AAXX_5/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 407857773 bwtLen: 407857774 sz: 101964444 bwtSz: 101964444 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12745556 offsSz: 50982224 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 910397 numSides: 1820794 numLines: 1820794 ebwtTotLen: 116530816 ebwtTotSz: 116530816 Total time for backward call to driver() for mirror index: 00:11:02