Settings: Output files: "/projects/NBL/HS1197/311NGAAXX_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/HS1197/311NGAAXX_3/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:17 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: 57372979 Using parameters --bmax 43029735 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 43029735 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:15 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: 00:00:05 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: 00:00:21 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: 00:00:18 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.86865e+07 (target: 43029734) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (43029735) 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 33676177 (Using difference cover) Sorting block time: 00:00:48 Returning block of 33676178 Getting block 2 of 8 Reserving size (43029735) 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 30038946 (Using difference cover) Sorting block time: 00:00:46 Returning block of 30038947 Getting block 3 of 8 Reserving size (43029735) 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 18366696 (Using difference cover) Sorting block time: 00:00:34 Returning block of 18366697 Getting block 4 of 8 Reserving size (43029735) 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: 00:00:09 Sorting block of length 31663504 (Using difference cover) Sorting block time: 00:00:56 Returning block of 31663505 Getting block 5 of 8 Reserving size (43029735) 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: 00:00:09 Sorting block of length 22599806 (Using difference cover) Sorting block time: 00:00:36 Returning block of 22599807 Getting block 6 of 8 Reserving size (43029735) 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: 00:00:10 Sorting block of length 38931887 (Using difference cover) Sorting block time: 00:01:07 Returning block of 38931888 Getting block 7 of 8 Reserving size (43029735) 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: 00:00:10 Sorting block of length 19733675 (Using difference cover) Sorting block time: 00:00:33 Returning block of 19733676 Getting block 8 of 8 Reserving size (43029735) 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 34481220 (Using difference cover) Sorting block time: 00:00:51 Returning block of 34481221 Exited Ebwt loop fchr[A]: 0 fchr[C]: 60272867 fchr[G]: 114928784 fchr[T]: 169269706 fchr[$]: 229491918 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 419332402 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_3/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 28686496 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_3/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 229491918 bwtLen: 229491919 sz: 57372980 bwtSz: 57372980 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 7171623 offsSz: 28686492 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 512259 numSides: 1024518 numLines: 1024518 ebwtTotLen: 65569152 ebwtTotSz: 65569152 Total time for call to driver() for forward index: 00:09:34 Reading reference sizes Time reading reference sizes: 00:00:08 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: 57372979 Using parameters --bmax 43029735 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 43029735 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:14 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: 00:00:05 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: 00:00:21 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 5; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:20 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: 00:00:22 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: 00:00:22 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.86865e+07 (target: 43029734) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (43029735) 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 9892491 (Using difference cover) Sorting block time: 00:00:11 Returning block of 9892492 Getting block 2 of 8 Reserving size (43029735) 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 40937198 (Using difference cover) Sorting block time: 00:01:06 Returning block of 40937199 Getting block 3 of 8 Reserving size (43029735) 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 29880688 (Using difference cover) Sorting block time: 00:00:50 Returning block of 29880689 Getting block 4 of 8 Reserving size (43029735) 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: 00:00:09 Sorting block of length 27235514 (Using difference cover) Sorting block time: 00:00:46 Returning block of 27235515 Getting block 5 of 8 Reserving size (43029735) 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: 00:00:09 Sorting block of length 41150103 (Using difference cover) Sorting block time: 00:01:11 Returning block of 41150104 Getting block 6 of 8 Reserving size (43029735) 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: 00:00:09 Sorting block of length 16772437 (Using difference cover) Sorting block time: 00:00:29 Returning block of 16772438 Getting block 7 of 8 Reserving size (43029735) 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: 00:00:10 Sorting block of length 37433051 (Using difference cover) Sorting block time: 00:00:59 Returning block of 37433052 Getting block 8 of 8 Reserving size (43029735) 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 26190429 (Using difference cover) Sorting block time: 00:00:37 Returning block of 26190430 Exited Ebwt loop fchr[A]: 0 fchr[C]: 60272867 fchr[G]: 114928784 fchr[T]: 169269706 fchr[$]: 229491918 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 419332402 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_3/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 28686496 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_3/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 229491918 bwtLen: 229491919 sz: 57372980 bwtSz: 57372980 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 7171623 offsSz: 28686492 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 512259 numSides: 1024518 numLines: 1024518 ebwtTotLen: 65569152 ebwtTotSz: 65569152 Total time for backward call to driver() for mirror index: 00:10:11