Settings: Output files: "/projects/NBL/HS1197/311NGAAXX_4/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/HS1197/311NGAAXX_4/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:24 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:15 bmax according to bmaxDivN setting: 58211156 Using parameters --bmax 43658367 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 43658367 --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: 00:00:04 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: 00:00:19 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: 00:00:15 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.32635e+07 (target: 43658366) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (43658367) 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 41729668 (Using difference cover) Sorting block time: 00:00:44 Returning block of 41729669 Getting block 2 of 7 Reserving size (43658367) 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 22715400 (Using difference cover) Sorting block time: 00:00:25 Returning block of 22715401 Getting block 3 of 7 Reserving size (43658367) 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 38108134 (Using difference cover) Sorting block time: 00:00:52 Returning block of 38108135 Getting block 4 of 7 Reserving size (43658367) 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 34638863 (Using difference cover) Sorting block time: 00:00:40 Returning block of 34638864 Getting block 5 of 7 Reserving size (43658367) 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 37791059 (Using difference cover) Sorting block time: 00:00:45 Returning block of 37791060 Getting block 6 of 7 Reserving size (43658367) 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 34600558 (Using difference cover) Sorting block time: 00:00:41 Returning block of 34600559 Getting block 7 of 7 Reserving size (43658367) 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 23260937 (Using difference cover) Sorting block time: 00:00:23 Returning block of 23260938 Exited Ebwt loop fchr[A]: 0 fchr[C]: 61017557 fchr[G]: 116842773 fchr[T]: 171556753 fchr[$]: 232844625 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 425336941 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_4/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 29105584 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_4/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 232844625 bwtLen: 232844626 sz: 58211157 bwtSz: 58211157 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 7276395 offsSz: 29105580 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 519743 numSides: 1039486 numLines: 1039486 ebwtTotLen: 66527104 ebwtTotSz: 66527104 Total time for call to driver() for forward index: 00:07:32 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: 00:00:13 bmax according to bmaxDivN setting: 58211156 Using parameters --bmax 43658367 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 43658367 --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: 00:00:04 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: 00:00:19 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: 00:00:14 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.88074e+07 (target: 43658366) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (43658367) 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 43417590 (Using difference cover) Sorting block time: 00:00:48 Returning block of 43417591 Getting block 2 of 6 Reserving size (43658367) 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 42681201 (Using difference cover) Sorting block time: 00:00:54 Returning block of 42681202 Getting block 3 of 6 Reserving size (43658367) 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 36748921 (Using difference cover) Sorting block time: 00:00:46 Returning block of 36748922 Getting block 4 of 6 Reserving size (43658367) 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 33822889 (Using difference cover) Sorting block time: 00:00:42 Returning block of 33822890 Getting block 5 of 6 Reserving size (43658367) 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 33940380 (Using difference cover) Sorting block time: 00:00:42 Returning block of 33940381 Getting block 6 of 6 Reserving size (43658367) 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 42233639 (Using difference cover) Sorting block time: 00:00:50 Returning block of 42233640 Exited Ebwt loop fchr[A]: 0 fchr[C]: 61017557 fchr[G]: 116842773 fchr[T]: 171556753 fchr[$]: 232844625 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 425336941 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_4/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 29105584 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_4/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 232844625 bwtLen: 232844626 sz: 58211157 bwtSz: 58211157 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 7276395 offsSz: 29105580 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 519743 numSides: 1039486 numLines: 1039486 ebwtTotLen: 66527104 ebwtTotSz: 66527104 Total time for backward call to driver() for mirror index: 00:07:06