Settings: Output files: "/scratch/8792987.1.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/8792987.1.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: 2711387 Using parameters --bmax 2033541 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2033541 --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 1, merged 5; 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: 1.35569e+06 (target: 2033540) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2033541) 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 1486798 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1486799 Getting block 2 of 8 Reserving size (2033541) 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 920469 (Using difference cover) Sorting block time: 00:00:00 Returning block of 920470 Getting block 3 of 8 Reserving size (2033541) 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 1892757 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1892758 Getting block 4 of 8 Reserving size (2033541) 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 1648151 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1648152 Getting block 5 of 8 Reserving size (2033541) 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 1066283 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1066284 Getting block 6 of 8 Reserving size (2033541) 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 1449584 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1449585 Getting block 7 of 8 Reserving size (2033541) 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 1714841 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1714842 Getting block 8 of 8 Reserving size (2033541) 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 666660 (Using difference cover) Sorting block time: 00:00:00 Returning block of 666661 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2694631 fchr[G]: 5411186 fchr[T]: 8128557 fchr[$]: 10845550 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22446705 bytes to primary EBWT file: /scratch/8792987.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2711392 bytes to secondary EBWT file: /scratch/8792987.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10845550 bwtLen: 10845551 sz: 2711388 bwtSz: 2711388 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 677847 offsSz: 2711388 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 56488 numLines: 56488 ebwtTotLen: 3615232 ebwtTotSz: 3615232 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: 2711387 Using parameters --bmax 2033541 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2033541 --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: 1.54936e+06 (target: 2033540) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2033541) 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 570059 (Using difference cover) Sorting block time: 00:00:00 Returning block of 570060 Getting block 2 of 7 Reserving size (2033541) 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 1801180 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1801181 Getting block 3 of 7 Reserving size (2033541) 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 1979273 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1979274 Getting block 4 of 7 Reserving size (2033541) 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 950726 (Using difference cover) Sorting block time: 00:00:00 Returning block of 950727 Getting block 5 of 7 Reserving size (2033541) 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 1821791 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1821792 Getting block 6 of 7 Reserving size (2033541) 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 1898613 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1898614 Getting block 7 of 7 Reserving size (2033541) 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 1823902 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1823903 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2694631 fchr[G]: 5411186 fchr[T]: 8128557 fchr[$]: 10845550 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22446705 bytes to primary EBWT file: /scratch/8792987.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2711392 bytes to secondary EBWT file: /scratch/8792987.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10845550 bwtLen: 10845551 sz: 2711388 bwtSz: 2711388 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 677847 offsSz: 2711388 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 56488 numLines: 56488 ebwtTotLen: 3615232 ebwtTotSz: 3615232 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:08