Settings: Output files: "/projects/NBL/HS1801/61074AAXX_8/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/HS1801/61074AAXX_8/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:40 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: 103290759 Using parameters --bmax 77468070 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 77468070 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:17 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: 00:00:07 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: 00:00:34 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: 00:00:27 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 2; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:26 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.90233e+07 (target: 77468069) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (77468070) 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 47067041 (Using difference cover) Sorting block time: 00:00:38 Returning block of 47067042 Getting block 2 of 7 Reserving size (77468070) 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 58229984 (Using difference cover) Sorting block time: 00:00:50 Returning block of 58229985 Getting block 3 of 7 Reserving size (77468070) 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 57340084 (Using difference cover) Sorting block time: 00:00:52 Returning block of 57340085 Getting block 4 of 7 Reserving size (77468070) 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 64544155 (Using difference cover) Sorting block time: 00:00:58 Returning block of 64544156 Getting block 5 of 7 Reserving size (77468070) 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 62222035 (Using difference cover) Sorting block time: 00:00:58 Returning block of 62222036 Getting block 6 of 7 Reserving size (77468070) 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 69141558 (Using difference cover) Sorting block time: 00:01:01 Returning block of 69141559 Getting block 7 of 7 Reserving size (77468070) 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 54618173 (Using difference cover) Sorting block time: 00:00:46 Returning block of 54618174 Exited Ebwt loop fchr[A]: 0 fchr[C]: 102804840 fchr[G]: 205120089 fchr[T]: 307022775 fchr[$]: 413163036 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 750294309 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_8/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 51645384 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_8/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 413163036 bwtLen: 413163037 sz: 103290759 bwtSz: 103290760 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12911345 offsSz: 51645380 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 922239 numSides: 1844478 numLines: 1844478 ebwtTotLen: 118046592 ebwtTotSz: 118046592 Total time for call to driver() for forward index: 00:11:33 Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:25 bmax according to bmaxDivN setting: 103290759 Using parameters --bmax 77468070 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 77468070 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:17 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 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: 00:00:34 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: 00:00:25 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.16454e+07 (target: 77468069) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (77468070) 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 36575512 (Using difference cover) Sorting block time: 00:00:28 Returning block of 36575513 Getting block 2 of 8 Reserving size (77468070) 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 62919840 (Using difference cover) Sorting block time: 00:00:55 Returning block of 62919841 Getting block 3 of 8 Reserving size (77468070) 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 40859687 (Using difference cover) Sorting block time: 00:00:36 Returning block of 40859688 Getting block 4 of 8 Reserving size (77468070) 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 42754667 (Using difference cover) Sorting block time: 00:00:40 Returning block of 42754668 Getting block 5 of 8 Reserving size (77468070) 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 62977108 (Using difference cover) Sorting block time: 00:00:57 Returning block of 62977109 Getting block 6 of 8 Reserving size (77468070) 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 63979375 (Using difference cover) Sorting block time: 00:00:58 Returning block of 63979376 Getting block 7 of 8 Reserving size (77468070) 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: 00:00:13 Sorting block of length 31395135 (Using difference cover) Sorting block time: 00:00:27 Returning block of 31395136 Getting block 8 of 8 Reserving size (77468070) 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 71701705 (Using difference cover) Sorting block time: 00:01:02 Returning block of 71701706 Exited Ebwt loop fchr[A]: 0 fchr[C]: 102804840 fchr[G]: 205120089 fchr[T]: 307022775 fchr[$]: 413163036 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 750294309 bytes to primary EBWT file: /projects/NBL/HS1801/61074AAXX_8/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 51645384 bytes to secondary EBWT file: /projects/NBL/HS1801/61074AAXX_8/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 413163036 bwtLen: 413163037 sz: 103290759 bwtSz: 103290760 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12911345 offsSz: 51645380 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 922239 numSides: 1844478 numLines: 1844478 ebwtTotLen: 118046592 ebwtTotSz: 118046592 Total time for backward call to driver() for mirror index: 00:10:48