Settings: Output files: "/projects/NBL/HS1195/30TTYAAXX_4/tophat/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/HS1195/30TTYAAXX_4/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:44 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:20 bmax according to bmaxDivN setting: 88371351 Using parameters --bmax 66278514 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 66278514 --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: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:06 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: 00:00:25 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: 00:00:20 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.89142e+07 (target: 66278513) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (66278514) 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 57454808 (Using difference cover) Sorting block time: 00:00:51 Returning block of 57454809 Getting block 2 of 6 Reserving size (66278514) 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 63181928 (Using difference cover) Sorting block time: 00:01:05 Returning block of 63181929 Getting block 3 of 6 Reserving size (66278514) 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: 00:00:11 Sorting block of length 52790269 (Using difference cover) Sorting block time: 00:01:00 Returning block of 52790270 Getting block 4 of 6 Reserving size (66278514) 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: 00:00:12 Sorting block of length 63677035 (Using difference cover) Sorting block time: 00:01:08 Returning block of 63677036 Getting block 5 of 6 Reserving size (66278514) 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: 00:00:12 Sorting block of length 63572947 (Using difference cover) Sorting block time: 00:01:16 Returning block of 63572948 Getting block 6 of 6 Reserving size (66278514) 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: 00:00:19 Sorting block of length 52808414 (Using difference cover) Sorting block time: 00:00:51 Returning block of 52808415 Exited Ebwt loop fchr[A]: 0 fchr[C]: 97297478 fchr[G]: 176440406 fchr[T]: 254862939 fchr[$]: 353485406 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 643037657 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_4/tophat/tmp/segment_juncs.1.ebwt Wrote 44185680 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_4/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 353485406 bwtLen: 353485407 sz: 88371352 bwtSz: 88371352 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 11046419 offsSz: 44185676 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 789030 numSides: 1578060 numLines: 1578060 ebwtTotLen: 100995840 ebwtTotSz: 100995840 Total time for call to driver() for forward index: 00:11:50 Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:29 bmax according to bmaxDivN setting: 88371351 Using parameters --bmax 66278514 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 66278514 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:17 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:06 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: 00:01:03 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: 00:00:26 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.04979e+07 (target: 66278513) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (66278514) 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 58068399 (Using difference cover) Sorting block time: 00:00:52 Returning block of 58068400 Getting block 2 of 7 Reserving size (66278514) 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 60553664 (Using difference cover) Sorting block time: 00:01:04 Returning block of 60553665 Getting block 3 of 7 Reserving size (66278514) 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: 00:00:26 Sorting block of length 65378298 (Using difference cover) Sorting block time: 00:01:11 Returning block of 65378299 Getting block 4 of 7 Reserving size (66278514) 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: 00:00:20 Sorting block of length 53723812 (Using difference cover) Sorting block time: 00:01:02 Returning block of 53723813 Getting block 5 of 7 Reserving size (66278514) 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: 00:00:12 Sorting block of length 42879379 (Using difference cover) Sorting block time: 00:00:45 Returning block of 42879380 Getting block 6 of 7 Reserving size (66278514) 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: 00:00:27 Sorting block of length 65353140 (Using difference cover) Sorting block time: 00:01:13 Returning block of 65353141 Getting block 7 of 7 Reserving size (66278514) 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 7528708 (Using difference cover) Sorting block time: 00:00:03 Returning block of 7528709 Exited Ebwt loop fchr[A]: 0 fchr[C]: 97297478 fchr[G]: 176440406 fchr[T]: 254862939 fchr[$]: 353485406 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 643037657 bytes to primary EBWT file: /projects/NBL/HS1195/30TTYAAXX_4/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 44185680 bytes to secondary EBWT file: /projects/NBL/HS1195/30TTYAAXX_4/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 353485406 bwtLen: 353485407 sz: 88371352 bwtSz: 88371352 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 11046419 offsSz: 44185676 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 789030 numSides: 1578060 numLines: 1578060 ebwtTotLen: 100995840 ebwtTotSz: 100995840 Total time for backward call to driver() for mirror index: 00:12:32