Settings: Output files: "/projects/NBL/HS1198/302P8AAXX_5/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/HS1198/302P8AAXX_5/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:13 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: 42343340 Using parameters --bmax 31757505 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 31757505 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:06 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: 00:00:02 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 Split 1, merged 2; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:10 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.41962e+07 (target: 31757504) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (31757505) 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 30895870 (Using difference cover) Sorting block time: 00:00:32 Returning block of 30895871 Getting block 2 of 7 Reserving size (31757505) 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 21265718 (Using difference cover) Sorting block time: 00:00:24 Returning block of 21265719 Getting block 3 of 7 Reserving size (31757505) 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 24973171 (Using difference cover) Sorting block time: 00:00:31 Returning block of 24973172 Getting block 4 of 7 Reserving size (31757505) 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 24306857 (Using difference cover) Sorting block time: 00:00:27 Returning block of 24306858 Getting block 5 of 7 Reserving size (31757505) 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 16587249 (Using difference cover) Sorting block time: 00:00:19 Returning block of 16587250 Getting block 6 of 7 Reserving size (31757505) 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 21945183 (Using difference cover) Sorting block time: 00:00:26 Returning block of 21945184 Getting block 7 of 7 Reserving size (31757505) 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 29399309 (Using difference cover) Sorting block time: 00:00:31 Returning block of 29399310 Exited Ebwt loop fchr[A]: 0 fchr[C]: 45371692 fchr[G]: 85303385 fchr[T]: 124192637 fchr[$]: 169373363 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 310231915 bytes to primary EBWT file: /projects/NBL/HS1198/302P8AAXX_5/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 21171676 bytes to secondary EBWT file: /projects/NBL/HS1198/302P8AAXX_5/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 169373363 bwtLen: 169373364 sz: 42343341 bwtSz: 42343341 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5292918 offsSz: 21171672 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 378066 numSides: 756132 numLines: 756132 ebwtTotLen: 48392448 ebwtTotSz: 48392448 Total time for call to driver() for forward index: 00:05:17 Reading reference sizes Time reading reference sizes: 00:00:03 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: 42343340 Using parameters --bmax 31757505 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 31757505 --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 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.11717e+07 (target: 31757504) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (31757505) 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 28774297 (Using difference cover) Sorting block time: 00:00:29 Returning block of 28774298 Getting block 2 of 8 Reserving size (31757505) 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 11368486 (Using difference cover) Sorting block time: 00:00:13 Returning block of 11368487 Getting block 3 of 8 Reserving size (31757505) 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 27257756 (Using difference cover) Sorting block time: 00:00:32 Returning block of 27257757 Getting block 4 of 8 Reserving size (31757505) 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 20721361 (Using difference cover) Sorting block time: 00:00:24 Returning block of 20721362 Getting block 5 of 8 Reserving size (31757505) 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 24942465 (Using difference cover) Sorting block time: 00:00:30 Returning block of 24942466 Getting block 6 of 8 Reserving size (31757505) 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 19995284 (Using difference cover) Sorting block time: 00:00:22 Returning block of 19995285 Getting block 7 of 8 Reserving size (31757505) 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 16032720 (Using difference cover) Sorting block time: 00:00:19 Returning block of 16032721 Getting block 8 of 8 Reserving size (31757505) 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 20280987 (Using difference cover) Sorting block time: 00:00:21 Returning block of 20280988 Exited Ebwt loop fchr[A]: 0 fchr[C]: 45371692 fchr[G]: 85303385 fchr[T]: 124192637 fchr[$]: 169373363 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 310231915 bytes to primary EBWT file: /projects/NBL/HS1198/302P8AAXX_5/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 21171676 bytes to secondary EBWT file: /projects/NBL/HS1198/302P8AAXX_5/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 169373363 bwtLen: 169373364 sz: 42343341 bwtSz: 42343341 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5292918 offsSz: 21171672 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 378066 numSides: 756132 numLines: 756132 ebwtTotLen: 48392448 ebwtTotSz: 48392448 Total time for backward call to driver() for mirror index: 00:05:02