Settings: Output files: "/scratch/8793243.1.c/tophat2/tmp/segment_juncs.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) 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: /scratch/8793243.1.c/tophat2/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 2748987 Using parameters --bmax 2061741 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2061741 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.37449e+06 (target: 2061740) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1499178 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1499179 Getting block 2 of 8 Reserving size (2061741) 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: 00:00:01 Sorting block of length 627504 (Using difference cover) Sorting block time: 00:00:00 Returning block of 627505 Getting block 3 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1803015 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1803016 Getting block 4 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1912632 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1912633 Getting block 5 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 787267 (Using difference cover) Sorting block time: 00:00:00 Returning block of 787268 Getting block 6 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1600302 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1600303 Getting block 7 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1621411 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1621412 Getting block 8 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1144634 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1144635 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2741592 fchr[G]: 5484063 fchr[T]: 8229904 fchr[$]: 10995950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22694375 bytes to primary EBWT file: /scratch/8793243.1.c/tophat2/tmp/segment_juncs.1.bt2 Wrote 2748992 bytes to secondary EBWT file: /scratch/8793243.1.c/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10995950 bwtLen: 10995951 sz: 2748988 bwtSz: 2748988 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 687247 offsSz: 2748988 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 57271 numLines: 57271 ebwtTotLen: 3665344 ebwtTotSz: 3665344 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:05 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2748987 Using parameters --bmax 2061741 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2061741 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 8; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 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: 00:00:01 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: 00:00:00 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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.37449e+06 (target: 2061740) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 704936 (Using difference cover) Sorting block time: 00:00:01 Returning block of 704937 Getting block 2 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1466979 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1466980 Getting block 3 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1577120 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1577121 Getting block 4 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 600515 (Using difference cover) Sorting block time: 00:00:00 Returning block of 600516 Getting block 5 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1892331 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1892332 Getting block 6 of 8 Reserving size (2061741) 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: 00:00:01 Sorting block of length 1472972 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1472973 Getting block 7 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 2012179 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2012180 Getting block 8 of 8 Reserving size (2061741) 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: 00:00:00 Sorting block of length 1268911 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1268912 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2741592 fchr[G]: 5484063 fchr[T]: 8229904 fchr[$]: 10995950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22694375 bytes to primary EBWT file: /scratch/8793243.1.c/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2748992 bytes to secondary EBWT file: /scratch/8793243.1.c/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10995950 bwtLen: 10995951 sz: 2748988 bwtSz: 2748988 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 687247 offsSz: 2748988 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 57271 numLines: 57271 ebwtTotLen: 3665344 ebwtTotSz: 3665344 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:06