Settings: Output files: "/projects/NBL/HS1197/311NGAAXX_3/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/HS1197/311NGAAXX_3/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:21 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:14 bmax according to bmaxDivN setting: 55419159 Using parameters --bmax 41564370 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 41564370 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:10 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:02 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:04 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: 00:00:17 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: 00:00:16 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.77096e+07 (target: 41564369) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (41564370) 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: 00:00:04 Sorting block of length 12320651 (Using difference cover) Sorting block time: 00:00:09 Returning block of 12320652 Getting block 2 of 8 Reserving size (41564370) 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: 00:00:06 Sorting block of length 33491040 (Using difference cover) Sorting block time: 00:00:40 Returning block of 33491041 Getting block 3 of 8 Reserving size (41564370) 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: 00:00:06 Sorting block of length 30354648 (Using difference cover) Sorting block time: 00:00:37 Returning block of 30354649 Getting block 4 of 8 Reserving size (41564370) 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 31062709 (Using difference cover) Sorting block time: 00:00:41 Returning block of 31062710 Getting block 5 of 8 Reserving size (41564370) 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: 00:00:07 Sorting block of length 38559670 (Using difference cover) Sorting block time: 00:00:48 Returning block of 38559671 Getting block 6 of 8 Reserving size (41564370) 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 31042149 (Using difference cover) Sorting block time: 00:00:39 Returning block of 31042150 Getting block 7 of 8 Reserving size (41564370) 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: 00:00:07 Sorting block of length 38838382 (Using difference cover) Sorting block time: 00:00:48 Returning block of 38838383 Getting block 8 of 8 Reserving size (41564370) 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: 00:00:04 Sorting block of length 6007382 (Using difference cover) Sorting block time: 00:00:04 Returning block of 6007383 Exited Ebwt loop fchr[A]: 0 fchr[C]: 58368743 fchr[G]: 111023822 fchr[T]: 163367924 fchr[$]: 221676638 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 405142511 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_3/tophat/tmp/segment_juncs.1.ebwt Wrote 27709584 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_3/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 221676638 bwtLen: 221676639 sz: 55419160 bwtSz: 55419160 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6927395 offsSz: 27709580 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 494814 numSides: 989628 numLines: 989628 ebwtTotLen: 63336192 ebwtTotSz: 63336192 Total time for call to driver() for forward index: 00:07:17 Reading reference sizes Time reading reference sizes: 00:00:04 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:13 bmax according to bmaxDivN setting: 55419159 Using parameters --bmax 41564370 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 41564370 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:09 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:02 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:03 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: 00:00:17 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: 00:00:14 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: 00:00:14 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: 00:00:17 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: 00:00:19 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Avg bucket size: 2.46307e+07 (target: 41564369) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (41564370) 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: 00:00:04 Sorting block of length 21730091 (Using difference cover) Sorting block time: 00:00:21 Returning block of 21730092 Getting block 2 of 9 Reserving size (41564370) 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: 00:00:06 Sorting block of length 31889791 (Using difference cover) Sorting block time: 00:00:38 Returning block of 31889792 Getting block 3 of 9 Reserving size (41564370) 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: 00:00:06 Sorting block of length 28191574 (Using difference cover) Sorting block time: 00:00:36 Returning block of 28191575 Getting block 4 of 9 Reserving size (41564370) 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: 00:00:06 Sorting block of length 17037983 (Using difference cover) Sorting block time: 00:00:22 Returning block of 17037984 Getting block 5 of 9 Reserving size (41564370) 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: 00:00:06 Sorting block of length 26821086 (Using difference cover) Sorting block time: 00:00:34 Returning block of 26821087 Getting block 6 of 9 Reserving size (41564370) 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: 00:00:07 Sorting block of length 18396438 (Using difference cover) Sorting block time: 00:00:24 Returning block of 18396439 Getting block 7 of 9 Reserving size (41564370) 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 28958900 (Using difference cover) Sorting block time: 00:00:34 Returning block of 28958901 Getting block 8 of 9 Reserving size (41564370) 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 40365086 (Using difference cover) Sorting block time: 00:00:48 Returning block of 40365087 Getting block 9 of 9 Reserving size (41564370) 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: 00:00:04 Sorting block of length 8285681 (Using difference cover) Sorting block time: 00:00:07 Returning block of 8285682 Exited Ebwt loop fchr[A]: 0 fchr[C]: 58368743 fchr[G]: 111023822 fchr[T]: 163367924 fchr[$]: 221676638 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 405142511 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_3/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 27709584 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_3/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 221676638 bwtLen: 221676639 sz: 55419160 bwtSz: 55419160 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6927395 offsSz: 27709580 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 494814 numSides: 989628 numLines: 989628 ebwtTotLen: 63336192 ebwtTotSz: 63336192 Total time for backward call to driver() for mirror index: 00:07:45