Settings: Output files: "/projects/NBL/HS1194/311L9AAXX_7/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_7/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:18 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: 43133718 Using parameters --bmax 32350289 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 32350289 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:08 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: 00:00:13 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: 00:00:11 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 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:12 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: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.91705e+07 (target: 32350288) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (32350289) 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 18266508 (Using difference cover) Sorting block time: 00:00:21 Returning block of 18266509 Getting block 2 of 9 Reserving size (32350289) 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 23238150 (Using difference cover) Sorting block time: 00:00:35 Returning block of 23238151 Getting block 3 of 9 Reserving size (32350289) 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 21017133 (Using difference cover) Sorting block time: 00:00:32 Returning block of 21017134 Getting block 4 of 9 Reserving size (32350289) 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 12409661 (Using difference cover) Sorting block time: 00:00:20 Returning block of 12409662 Getting block 5 of 9 Reserving size (32350289) 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 27353883 (Using difference cover) Sorting block time: 00:00:41 Returning block of 27353884 Getting block 6 of 9 Reserving size (32350289) 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 26948082 (Using difference cover) Sorting block time: 00:00:40 Returning block of 26948083 Getting block 7 of 9 Reserving size (32350289) 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 7676972 (Using difference cover) Sorting block time: 00:00:11 Returning block of 7676973 Getting block 8 of 9 Reserving size (32350289) 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 31575042 (Using difference cover) Sorting block time: 00:00:46 Returning block of 31575043 Getting block 9 of 9 Reserving size (32350289) 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 4049433 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4049434 Exited Ebwt loop fchr[A]: 0 fchr[C]: 44528866 fchr[G]: 87888038 fchr[T]: 128012823 fchr[$]: 172534872 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 315784466 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_7/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 21566864 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_7/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 172534872 bwtLen: 172534873 sz: 43133718 bwtSz: 43133719 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5391715 offsSz: 21566860 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 385123 numSides: 770246 numLines: 770246 ebwtTotLen: 49295744 ebwtTotSz: 49295744 Total time for call to driver() for forward index: 00:07:00 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: 43133718 Using parameters --bmax 32350289 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 32350289 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:08 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: 00:00:13 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: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.46478e+07 (target: 32350288) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (32350289) 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 31885802 (Using difference cover) Sorting block time: 00:00:42 Returning block of 31885803 Getting block 2 of 7 Reserving size (32350289) 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 30746264 (Using difference cover) Sorting block time: 00:00:47 Returning block of 30746265 Getting block 3 of 7 Reserving size (32350289) 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 13882008 (Using difference cover) Sorting block time: 00:00:20 Returning block of 13882009 Getting block 4 of 7 Reserving size (32350289) 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 26886011 (Using difference cover) Sorting block time: 00:00:42 Returning block of 26886012 Getting block 5 of 7 Reserving size (32350289) 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 22653157 (Using difference cover) Sorting block time: 00:00:33 Returning block of 22653158 Getting block 6 of 7 Reserving size (32350289) 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 30901328 (Using difference cover) Sorting block time: 00:00:44 Returning block of 30901329 Getting block 7 of 7 Reserving size (32350289) 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 15580296 (Using difference cover) Sorting block time: 00:00:19 Returning block of 15580297 Exited Ebwt loop fchr[A]: 0 fchr[C]: 44528866 fchr[G]: 87888038 fchr[T]: 128012823 fchr[$]: 172534872 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 315784466 bytes to primary EBWT file: /projects/NBL/HS1194/311L9AAXX_7/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 21566864 bytes to secondary EBWT file: /projects/NBL/HS1194/311L9AAXX_7/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 172534872 bwtLen: 172534873 sz: 43133718 bwtSz: 43133719 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5391715 offsSz: 21566860 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 385123 numSides: 770246 numLines: 770246 ebwtTotLen: 49295744 ebwtTotSz: 49295744 Total time for backward call to driver() for mirror index: 00:06:01