Settings: Output files: "/scratch/9351455.1.linga/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/9351455.1.linga/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: 00:00:01 bmax according to bmaxDivN setting: 4450088 Using parameters --bmax 3337566 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3337566 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 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 1, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.54291e+06 (target: 3337565) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3337566) 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 3141956 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3141957 Getting block 2 of 7 Reserving size (3337566) 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 2969977 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2969978 Getting block 3 of 7 Reserving size (3337566) 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 436086 (Using difference cover) Sorting block time: 00:00:00 Returning block of 436087 Getting block 4 of 7 Reserving size (3337566) 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 2986398 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2986399 Getting block 5 of 7 Reserving size (3337566) 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 2671552 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2671553 Getting block 6 of 7 Reserving size (3337566) 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 2717238 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2717239 Getting block 7 of 7 Reserving size (3337566) 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 2877140 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2877141 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4413991 fchr[G]: 8921442 fchr[T]: 13396825 fchr[$]: 17800353 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33161239 bytes to primary EBWT file: /scratch/9351455.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 4450096 bytes to secondary EBWT file: /scratch/9351455.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17800353 bwtLen: 17800354 sz: 4450089 bwtSz: 4450089 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1112523 offsSz: 4450092 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 92711 numLines: 92711 ebwtTotLen: 5933504 ebwtTotSz: 5933504 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:22 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: 4450088 Using parameters --bmax 3337566 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3337566 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:01 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 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.54291e+06 (target: 3337565) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3337566) 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 3076968 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3076969 Getting block 2 of 7 Reserving size (3337566) 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 2243127 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2243128 Getting block 3 of 7 Reserving size (3337566) 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 3291073 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3291074 Getting block 4 of 7 Reserving size (3337566) 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 2749386 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2749387 Getting block 5 of 7 Reserving size (3337566) 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 1688200 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1688201 Getting block 6 of 7 Reserving size (3337566) 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 2468567 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2468568 Getting block 7 of 7 Reserving size (3337566) 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 2283026 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2283027 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4413991 fchr[G]: 8921442 fchr[T]: 13396825 fchr[$]: 17800353 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33161239 bytes to primary EBWT file: /scratch/9351455.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 4450096 bytes to secondary EBWT file: /scratch/9351455.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17800353 bwtLen: 17800354 sz: 4450089 bwtSz: 4450089 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1112523 offsSz: 4450092 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 92711 numLines: 92711 ebwtTotLen: 5933504 ebwtTotSz: 5933504 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:22