Settings: Output files: "/projects/NBL/HS1797/616GYAAXX_1/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/HS1797/616GYAAXX_1/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:01:23 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:28 bmax according to bmaxDivN setting: 101962564 Using parameters --bmax 76471923 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 76471923 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:25 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:06 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:11 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 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:30 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: 00:00:28 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 6.7975e+07 (target: 76471922) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (76471923) 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 66562076 (Using difference cover) Sorting block time: 00:01:23 Returning block of 66562077 Getting block 2 of 6 Reserving size (76471923) 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 70148600 (Using difference cover) Sorting block time: 00:01:30 Returning block of 70148601 Getting block 3 of 6 Reserving size (76471923) 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 70861280 (Using difference cover) Sorting block time: 00:01:36 Returning block of 70861281 Getting block 4 of 6 Reserving size (76471923) 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: 00:00:16 Sorting block of length 74180262 (Using difference cover) Sorting block time: 00:01:40 Returning block of 74180263 Getting block 5 of 6 Reserving size (76471923) 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: 00:00:17 Sorting block of length 57917961 (Using difference cover) Sorting block time: 00:01:16 Returning block of 57917962 Getting block 6 of 6 Reserving size (76471923) 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 68180072 (Using difference cover) Sorting block time: 00:01:26 Returning block of 68180073 Exited Ebwt loop fchr[A]: 0 fchr[C]: 100823207 fchr[G]: 201958861 fchr[T]: 302886803 fchr[$]: 407850256 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 741312040 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_1/tophat/tmp/segment_juncs.1.ebwt Wrote 50981288 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_1/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 407850256 bwtLen: 407850257 sz: 101962564 bwtSz: 101962565 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12745321 offsSz: 50981284 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 910381 numSides: 1820762 numLines: 1820762 ebwtTotLen: 116528768 ebwtTotSz: 116528768 Total time for call to driver() for forward index: 00:17:21 Reading reference sizes Time reading reference sizes: 00:00:12 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:32 bmax according to bmaxDivN setting: 101962564 Using parameters --bmax 76471923 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 76471923 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:26 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: 00:00:11 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: 00:00:35 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: 00:00:30 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.82643e+07 (target: 76471922) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (76471923) 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 47222023 (Using difference cover) Sorting block time: 00:00:57 Returning block of 47222024 Getting block 2 of 7 Reserving size (76471923) 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 60216060 (Using difference cover) Sorting block time: 00:01:16 Returning block of 60216061 Getting block 3 of 7 Reserving size (76471923) 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 74251824 (Using difference cover) Sorting block time: 00:01:41 Returning block of 74251825 Getting block 4 of 7 Reserving size (76471923) 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 21994525 (Using difference cover) Sorting block time: 00:00:29 Returning block of 21994526 Getting block 5 of 7 Reserving size (76471923) 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: 00:00:17 Sorting block of length 70778240 (Using difference cover) Sorting block time: 00:01:35 Returning block of 70778241 Getting block 6 of 7 Reserving size (76471923) 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: 00:00:18 Sorting block of length 74982409 (Using difference cover) Sorting block time: 00:01:37 Returning block of 74982410 Getting block 7 of 7 Reserving size (76471923) 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 58405169 (Using difference cover) Sorting block time: 00:01:13 Returning block of 58405170 Exited Ebwt loop fchr[A]: 0 fchr[C]: 100823207 fchr[G]: 201958861 fchr[T]: 302886803 fchr[$]: 407850256 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 741312040 bytes to primary EBWT file: /projects/NBL/HS1797/616GYAAXX_1/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 50981288 bytes to secondary EBWT file: /projects/NBL/HS1797/616GYAAXX_1/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 407850256 bwtLen: 407850257 sz: 101962564 bwtSz: 101962565 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 12745321 offsSz: 50981284 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 910381 numSides: 1820762 numLines: 1820762 ebwtTotLen: 116528768 ebwtTotSz: 116528768 Total time for backward call to driver() for mirror index: 00:15:46