Settings: Output files: "/projects/NBL/HS1801/61B1HAAXX_8/tophat/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/HS1801/61B1HAAXX_8/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:01:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:24 bmax according to bmaxDivN setting: 100448347 Using parameters --bmax 75336261 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 75336261 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:15 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: 00:00:06 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 Avg bucket size: 5.73991e+07 (target: 75336260) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (75336261) 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 46532457 (Using difference cover) Sorting block time: 00:00:40 Returning block of 46532458 Getting block 2 of 7 Reserving size (75336261) 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 67337959 (Using difference cover) Sorting block time: 00:00:59 Returning block of 67337960 Getting block 3 of 7 Reserving size (75336261) 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 65778805 (Using difference cover) Sorting block time: 00:01:05 Returning block of 65778806 Getting block 4 of 7 Reserving size (75336261) 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 54238028 (Using difference cover) Sorting block time: 00:00:51 Returning block of 54238029 Getting block 5 of 7 Reserving size (75336261) 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 27749403 (Using difference cover) Sorting block time: 00:00:26 Returning block of 27749404 Getting block 6 of 7 Reserving size (75336261) 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 72729636 (Using difference cover) Sorting block time: 00:01:04 Returning block of 72729637 Getting block 7 of 7 Reserving size (75336261) 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 67427094 (Using difference cover) Sorting block time: 00:00:57 Returning block of 67427095 Exited Ebwt loop fchr[A]: 0 fchr[C]: 99684834 fchr[G]: 199530838 fchr[T]: 299109385 fchr[$]: 401793388 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 729797897 bytes to primary EBWT file: /projects/NBL/HS1801/61B1HAAXX_8/tophat/tmp/segment_juncs.1.ebwt Wrote 50224180 bytes to secondary EBWT file: /projects/NBL/HS1801/61B1HAAXX_8/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 401793388 bwtLen: 401793389 sz: 100448347 bwtSz: 100448348 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12556044 offsSz: 50224176 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 896861 numSides: 1793722 numLines: 1793722 ebwtTotLen: 114798208 ebwtTotSz: 114798208 Total time for call to driver() for forward index: 00:11:40 Reading reference sizes Time reading reference sizes: 00:00:07 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:24 bmax according to bmaxDivN setting: 100448347 Using parameters --bmax 75336261 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 75336261 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:16 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: 00:00:07 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: 00:00:37 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: 5.02242e+07 (target: 75336260) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (75336261) 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 55080388 (Using difference cover) Sorting block time: 00:00:48 Returning block of 55080389 Getting block 2 of 8 Reserving size (75336261) 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 37519591 (Using difference cover) Sorting block time: 00:00:33 Returning block of 37519592 Getting block 3 of 8 Reserving size (75336261) 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 64323217 (Using difference cover) Sorting block time: 00:01:02 Returning block of 64323218 Getting block 4 of 8 Reserving size (75336261) 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 69213718 (Using difference cover) Sorting block time: 00:01:02 Returning block of 69213719 Getting block 5 of 8 Reserving size (75336261) 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 8754689 (Using difference cover) Sorting block time: 00:00:09 Returning block of 8754690 Getting block 6 of 8 Reserving size (75336261) 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 73991113 (Using difference cover) Sorting block time: 00:01:10 Returning block of 73991114 Getting block 7 of 8 Reserving size (75336261) 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 65514684 (Using difference cover) Sorting block time: 00:00:59 Returning block of 65514685 Getting block 8 of 8 Reserving size (75336261) 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 27395981 (Using difference cover) Sorting block time: 00:00:22 Returning block of 27395982 Exited Ebwt loop fchr[A]: 0 fchr[C]: 99684834 fchr[G]: 199530838 fchr[T]: 299109385 fchr[$]: 401793388 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 729797897 bytes to primary EBWT file: /projects/NBL/HS1801/61B1HAAXX_8/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 50224180 bytes to secondary EBWT file: /projects/NBL/HS1801/61B1HAAXX_8/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 401793388 bwtLen: 401793389 sz: 100448347 bwtSz: 100448348 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12556044 offsSz: 50224176 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 896861 numSides: 1793722 numLines: 1793722 ebwtTotLen: 114798208 ebwtTotSz: 114798208 Total time for backward call to driver() for mirror index: 00:11:14