Settings: Output files: "/projects/NBL/HS1194/311L9AAXX_3/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/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs.fa 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: 00:00:10 bmax according to bmaxDivN setting: 39874876 Using parameters --bmax 29906157 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 29906157 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:07 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 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: 00:00:13 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: 00:00:09 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.99374e+07 (target: 29906156) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (29906157) 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 22448857 (Using difference cover) Sorting block time: 00:00:24 Returning block of 22448858 Getting block 2 of 8 Reserving size (29906157) 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: 00:00:05 Sorting block of length 26071683 (Using difference cover) Sorting block time: 00:00:32 Returning block of 26071684 Getting block 3 of 8 Reserving size (29906157) 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: 00:00:05 Sorting block of length 19784395 (Using difference cover) Sorting block time: 00:00:25 Returning block of 19784396 Getting block 4 of 8 Reserving size (29906157) 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: 00:00:05 Sorting block of length 23235845 (Using difference cover) Sorting block time: 00:00:28 Returning block of 23235846 Getting block 5 of 8 Reserving size (29906157) 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 22852874 (Using difference cover) Sorting block time: 00:00:28 Returning block of 22852875 Getting block 6 of 8 Reserving size (29906157) 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 7780958 (Using difference cover) Sorting block time: 00:00:09 Returning block of 7780959 Getting block 7 of 8 Reserving size (29906157) 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 22378463 (Using difference cover) Sorting block time: 00:00:27 Returning block of 22378464 Getting block 8 of 8 Reserving size (29906157) 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: 00:00:03 Sorting block of length 14946424 (Using difference cover) Sorting block time: 00:00:16 Returning block of 14946425 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41332768 fchr[G]: 80864740 fchr[T]: 118003926 fchr[$]: 159499506 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 292475170 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 19937444 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 159499506 bwtLen: 159499507 sz: 39874877 bwtSz: 39874877 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4984360 offsSz: 19937440 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 356026 numSides: 712052 numLines: 712052 ebwtTotLen: 45571328 ebwtTotSz: 45571328 Total time for call to driver() for forward index: 00:05:10 Reading reference sizes Time reading reference sizes: 00:00:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:09 bmax according to bmaxDivN setting: 39874876 Using parameters --bmax 29906157 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 29906157 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:07 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:02 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: 00:00:14 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: 00:00:10 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.27856e+07 (target: 29906156) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (29906157) 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: 00:00:03 Sorting block of length 24724333 (Using difference cover) Sorting block time: 00:00:28 Returning block of 24724334 Getting block 2 of 7 Reserving size (29906157) 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: 00:00:05 Sorting block of length 29830648 (Using difference cover) Sorting block time: 00:00:37 Returning block of 29830649 Getting block 3 of 7 Reserving size (29906157) 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: 00:00:05 Sorting block of length 24114594 (Using difference cover) Sorting block time: 00:00:30 Returning block of 24114595 Getting block 4 of 7 Reserving size (29906157) 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: 00:00:05 Sorting block of length 9113141 (Using difference cover) Sorting block time: 00:00:09 Returning block of 9113142 Getting block 5 of 7 Reserving size (29906157) 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 28986356 (Using difference cover) Sorting block time: 00:00:36 Returning block of 28986357 Getting block 6 of 7 Reserving size (29906157) 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 21817338 (Using difference cover) Sorting block time: 00:00:26 Returning block of 21817339 Getting block 7 of 7 Reserving size (29906157) 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: 00:00:03 Sorting block of length 20913090 (Using difference cover) Sorting block time: 00:00:23 Returning block of 20913091 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41332768 fchr[G]: 80864740 fchr[T]: 118003926 fchr[$]: 159499506 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 292475170 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 19937444 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 159499506 bwtLen: 159499507 sz: 39874877 bwtSz: 39874877 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4984360 offsSz: 19937440 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 356026 numSides: 712052 numLines: 712052 ebwtTotLen: 45571328 ebwtTotSz: 45571328 Total time for backward call to driver() for mirror index: 00:04:55