Settings: Output files: "/projects/NBL/HS1196/3153YAAXX_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/HS1196/3153YAAXX_5/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: 40569216 Using parameters --bmax 30426912 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 30426912 --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 1, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:09 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.31824e+07 (target: 30426911) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (30426912) 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 26768433 (Using difference cover) Sorting block time: 00:00:28 Returning block of 26768434 Getting block 2 of 7 Reserving size (30426912) 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 24555199 (Using difference cover) Sorting block time: 00:00:29 Returning block of 24555200 Getting block 3 of 7 Reserving size (30426912) 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 29998771 (Using difference cover) Sorting block time: 00:00:36 Returning block of 29998772 Getting block 4 of 7 Reserving size (30426912) 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 28294189 (Using difference cover) Sorting block time: 00:00:33 Returning block of 28294190 Getting block 5 of 7 Reserving size (30426912) 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 12635290 (Using difference cover) Sorting block time: 00:00:15 Returning block of 12635291 Getting block 6 of 7 Reserving size (30426912) 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 23866232 (Using difference cover) Sorting block time: 00:00:26 Returning block of 23866233 Getting block 7 of 7 Reserving size (30426912) 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 16158744 (Using difference cover) Sorting block time: 00:00:16 Returning block of 16158745 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41041592 fchr[G]: 81484266 fchr[T]: 121255450 fchr[$]: 162276864 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 297502838 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_5/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 20284616 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_5/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 162276864 bwtLen: 162276865 sz: 40569216 bwtSz: 40569217 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5071153 offsSz: 20284612 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 362226 numSides: 724452 numLines: 724452 ebwtTotLen: 46364928 ebwtTotSz: 46364928 Total time for call to driver() for forward index: 00:04:57 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: 40569216 Using parameters --bmax 30426912 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 30426912 --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: 00:00:12 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: 00:00:09 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: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.70461e+07 (target: 30426911) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (30426912) 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 25360512 (Using difference cover) Sorting block time: 00:00:26 Returning block of 25360513 Getting block 2 of 6 Reserving size (30426912) 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 26206800 (Using difference cover) Sorting block time: 00:00:29 Returning block of 26206801 Getting block 3 of 6 Reserving size (30426912) 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 26898638 (Using difference cover) Sorting block time: 00:00:32 Returning block of 26898639 Getting block 4 of 6 Reserving size (30426912) 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 30416246 (Using difference cover) Sorting block time: 00:00:36 Returning block of 30416247 Getting block 5 of 6 Reserving size (30426912) 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 28224828 (Using difference cover) Sorting block time: 00:00:31 Returning block of 28224829 Getting block 6 of 6 Reserving size (30426912) 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 25169835 (Using difference cover) Sorting block time: 00:00:26 Returning block of 25169836 Exited Ebwt loop fchr[A]: 0 fchr[C]: 41041592 fchr[G]: 81484266 fchr[T]: 121255450 fchr[$]: 162276864 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 297502838 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_5/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 20284616 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_5/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 162276864 bwtLen: 162276865 sz: 40569216 bwtSz: 40569217 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5071153 offsSz: 20284612 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 362226 numSides: 724452 numLines: 724452 ebwtTotLen: 46364928 ebwtTotSz: 46364928 Total time for backward call to driver() for mirror index: 00:04:53