Settings: Output files: "/scratch/8793365.1.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/8793365.1.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: 2522650 Using parameters --bmax 1891988 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1891988 --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 Avg bucket size: 1.44151e+06 (target: 1891987) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1891988) 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 1682690 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1682691 Getting block 2 of 7 Reserving size (1891988) 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 1580534 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1580535 Getting block 3 of 7 Reserving size (1891988) 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 1529740 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1529741 Getting block 4 of 7 Reserving size (1891988) 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 1481930 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1481931 Getting block 5 of 7 Reserving size (1891988) 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 1568037 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1568038 Getting block 6 of 7 Reserving size (1891988) 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 1805290 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1805291 Getting block 7 of 7 Reserving size (1891988) 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 442373 (Using difference cover) Sorting block time: 00:00:00 Returning block of 442374 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2504688 fchr[G]: 5041002 fchr[T]: 7578152 fchr[$]: 10090600 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21174172 bytes to primary EBWT file: /scratch/8793365.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2522656 bytes to secondary EBWT file: /scratch/8793365.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10090600 bwtLen: 10090601 sz: 2522650 bwtSz: 2522651 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630663 offsSz: 2522652 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52556 numLines: 52556 ebwtTotLen: 3363584 ebwtTotSz: 3363584 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:07 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2522650 Using parameters --bmax 1891988 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1891988 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.26132e+06 (target: 1891987) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1891988) 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 1114070 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1114071 Getting block 2 of 8 Reserving size (1891988) 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 1522140 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1522141 Getting block 3 of 8 Reserving size (1891988) 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 918621 (Using difference cover) Sorting block time: 00:00:00 Returning block of 918622 Getting block 4 of 8 Reserving size (1891988) 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 1797450 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1797451 Getting block 5 of 8 Reserving size (1891988) 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 1523096 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1523097 Getting block 6 of 8 Reserving size (1891988) 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 992698 (Using difference cover) Sorting block time: 00:00:00 Returning block of 992699 Getting block 7 of 8 Reserving size (1891988) 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 1665775 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1665776 Getting block 8 of 8 Reserving size (1891988) 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 556743 (Using difference cover) Sorting block time: 00:00:00 Returning block of 556744 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2504688 fchr[G]: 5041002 fchr[T]: 7578152 fchr[$]: 10090600 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21174172 bytes to primary EBWT file: /scratch/8793365.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2522656 bytes to secondary EBWT file: /scratch/8793365.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10090600 bwtLen: 10090601 sz: 2522650 bwtSz: 2522651 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630663 offsSz: 2522652 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52556 numLines: 52556 ebwtTotLen: 3363584 ebwtTotSz: 3363584 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:06