Settings: Output files: "/scratch/8793097.1.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/8793097.1.linga/tophat2/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:01 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: 2803737 Using parameters --bmax 2102803 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2102803 --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: 1.60213e+06 (target: 2102802) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2102803) 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 1905055 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1905056 Getting block 2 of 7 Reserving size (2102803) 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 1098965 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1098966 Getting block 3 of 7 Reserving size (2102803) 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 1558065 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1558066 Getting block 4 of 7 Reserving size (2102803) 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 2077812 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2077813 Getting block 5 of 7 Reserving size (2102803) 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 1922838 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1922839 Getting block 6 of 7 Reserving size (2102803) 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 1690230 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1690231 Getting block 7 of 7 Reserving size (2102803) 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 961979 (Using difference cover) Sorting block time: 00:00:00 Returning block of 961980 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2784055 fchr[G]: 5594198 fchr[T]: 8398814 fchr[$]: 11214950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23069063 bytes to primary EBWT file: /scratch/8793097.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2803744 bytes to secondary EBWT file: /scratch/8793097.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11214950 bwtLen: 11214951 sz: 2803738 bwtSz: 2803738 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 700935 offsSz: 2803740 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58412 numLines: 58412 ebwtTotLen: 3738368 ebwtTotSz: 3738368 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: 2803737 Using parameters --bmax 2102803 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2102803 --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 6; 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.2461e+06 (target: 2102802) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2102803) 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 1030232 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1030233 Getting block 2 of 9 Reserving size (2102803) 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 1661028 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1661029 Getting block 3 of 9 Reserving size (2102803) 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 540224 (Using difference cover) Sorting block time: 00:00:00 Returning block of 540225 Getting block 4 of 9 Reserving size (2102803) 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 1860128 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1860129 Getting block 5 of 9 Reserving size (2102803) 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 564951 (Using difference cover) Sorting block time: 00:00:00 Returning block of 564952 Getting block 6 of 9 Reserving size (2102803) 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 1777447 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1777448 Getting block 7 of 9 Reserving size (2102803) 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 1421369 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1421370 Getting block 8 of 9 Reserving size (2102803) 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 1526429 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1526430 Getting block 9 of 9 Reserving size (2102803) 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 833134 (Using difference cover) Sorting block time: 00:00:00 Returning block of 833135 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2784055 fchr[G]: 5594198 fchr[T]: 8398814 fchr[$]: 11214950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23069063 bytes to primary EBWT file: /scratch/8793097.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2803744 bytes to secondary EBWT file: /scratch/8793097.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11214950 bwtLen: 11214951 sz: 2803738 bwtSz: 2803738 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 700935 offsSz: 2803740 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58412 numLines: 58412 ebwtTotLen: 3738368 ebwtTotSz: 3738368 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10