Settings: Output files: "/scratch/8793381.1.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/8793381.1.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: 2557350 Using parameters --bmax 1918013 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1918013 --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: 00:00:01 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 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.46134e+06 (target: 1918012) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1918013) 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 912526 (Using difference cover) Sorting block time: 00:00:00 Returning block of 912527 Getting block 2 of 7 Reserving size (1918013) 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 1857328 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1857329 Getting block 3 of 7 Reserving size (1918013) 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 1742752 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1742753 Getting block 4 of 7 Reserving size (1918013) 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 1639893 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1639894 Getting block 5 of 7 Reserving size (1918013) 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 837670 (Using difference cover) Sorting block time: 00:00:00 Returning block of 837671 Getting block 6 of 7 Reserving size (1918013) 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 1902846 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1902847 Getting block 7 of 7 Reserving size (1918013) 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 1336379 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1336380 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2532109 fchr[G]: 5109815 fchr[T]: 7686036 fchr[$]: 10229400 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21409701 bytes to primary EBWT file: /scratch/8793381.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2557356 bytes to secondary EBWT file: /scratch/8793381.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10229400 bwtLen: 10229401 sz: 2557350 bwtSz: 2557351 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 639338 offsSz: 2557352 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 53279 numLines: 53279 ebwtTotLen: 3409856 ebwtTotSz: 3409856 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:08 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: 2557350 Using parameters --bmax 1918013 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1918013 --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 Split 2, 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: 1.46134e+06 (target: 1918012) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1918013) 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 651879 (Using difference cover) Sorting block time: 00:00:00 Returning block of 651880 Getting block 2 of 7 Reserving size (1918013) 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 1893716 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1893717 Getting block 3 of 7 Reserving size (1918013) 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 1701697 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1701698 Getting block 4 of 7 Reserving size (1918013) 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 1763792 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1763793 Getting block 5 of 7 Reserving size (1918013) 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 1439383 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1439384 Getting block 6 of 7 Reserving size (1918013) 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 1089182 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1089183 Getting block 7 of 7 Reserving size (1918013) 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 1689745 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1689746 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2532109 fchr[G]: 5109815 fchr[T]: 7686036 fchr[$]: 10229400 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21409701 bytes to primary EBWT file: /scratch/8793381.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2557356 bytes to secondary EBWT file: /scratch/8793381.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10229400 bwtLen: 10229401 sz: 2557350 bwtSz: 2557351 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 639338 offsSz: 2557352 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 53279 numLines: 53279 ebwtTotLen: 3409856 ebwtTotSz: 3409856 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:07