Settings: Output files: "/scratch/8793102.1.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/8793102.1.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: 2724337 Using parameters --bmax 2043253 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2043253 --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: 1.55676e+06 (target: 2043252) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2043253) 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 2030910 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2030911 Getting block 2 of 7 Reserving size (2043253) 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 1471116 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1471117 Getting block 3 of 7 Reserving size (2043253) 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 2024416 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2024417 Getting block 4 of 7 Reserving size (2043253) 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 1574752 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1574753 Getting block 5 of 7 Reserving size (2043253) 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 1385339 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1385340 Getting block 6 of 7 Reserving size (2043253) 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 1468610 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1468611 Getting block 7 of 7 Reserving size (2043253) 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 942201 (Using difference cover) Sorting block time: 00:00:00 Returning block of 942202 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2719399 fchr[G]: 5440746 fchr[T]: 8157709 fchr[$]: 10897350 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22522897 bytes to primary EBWT file: /scratch/8793102.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2724344 bytes to secondary EBWT file: /scratch/8793102.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10897350 bwtLen: 10897351 sz: 2724338 bwtSz: 2724338 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 681085 offsSz: 2724340 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 56758 numLines: 56758 ebwtTotLen: 3632512 ebwtTotSz: 3632512 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:09 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: 2724337 Using parameters --bmax 2043253 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2043253 --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: 1.55676e+06 (target: 2043252) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2043253) 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 1584980 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1584981 Getting block 2 of 7 Reserving size (2043253) 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 1355424 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1355425 Getting block 3 of 7 Reserving size (2043253) 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 1979250 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1979251 Getting block 4 of 7 Reserving size (2043253) 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 1764639 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1764640 Getting block 5 of 7 Reserving size (2043253) 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 1111305 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1111306 Getting block 6 of 7 Reserving size (2043253) 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 1737185 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1737186 Getting block 7 of 7 Reserving size (2043253) 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 1364561 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1364562 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2719399 fchr[G]: 5440746 fchr[T]: 8157709 fchr[$]: 10897350 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22522897 bytes to primary EBWT file: /scratch/8793102.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2724344 bytes to secondary EBWT file: /scratch/8793102.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10897350 bwtLen: 10897351 sz: 2724338 bwtSz: 2724338 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 681085 offsSz: 2724340 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 56758 numLines: 56758 ebwtTotLen: 3632512 ebwtTotSz: 3632512 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:09