Settings: Output files: "./tophat_out/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: ./tophat_out/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: 00:00:02 bmax according to bmaxDivN setting: 22237368 Using parameters --bmax 16678026 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 16678026 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:02 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: 00:00:04 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: 00:00:04 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.11187e+07 (target: 16678025) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (16678026) 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 12213691 (Using difference cover) Sorting block time: 00:00:04 Returning block of 12213692 Getting block 2 of 8 Reserving size (16678026) 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 9355331 (Using difference cover) Sorting block time: 00:00:03 Returning block of 9355332 Getting block 3 of 8 Reserving size (16678026) 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 8262110 (Using difference cover) Sorting block time: 00:00:03 Returning block of 8262111 Getting block 4 of 8 Reserving size (16678026) 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 8749425 (Using difference cover) Sorting block time: 00:00:03 Returning block of 8749426 Getting block 5 of 8 Reserving size (16678026) 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 12635770 (Using difference cover) Sorting block time: 00:00:04 Returning block of 12635771 Getting block 6 of 8 Reserving size (16678026) 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: 00:00:02 Sorting block of length 12104795 (Using difference cover) Sorting block time: 00:00:04 Returning block of 12104796 Getting block 7 of 8 Reserving size (16678026) 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: 00:00:02 Sorting block of length 12340423 (Using difference cover) Sorting block time: 00:00:03 Returning block of 12340424 Getting block 8 of 8 Reserving size (16678026) 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 13287923 (Using difference cover) Sorting block time: 00:00:04 Returning block of 13287924 Exited Ebwt loop fchr[A]: 0 fchr[C]: 28922758 fchr[G]: 44882892 fchr[T]: 60810796 fchr[$]: 88949475 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 149399405 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.1.bt2 Wrote 22237376 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 88949475 bwtLen: 88949476 sz: 22237369 bwtSz: 22237369 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5559343 offsSz: 22237372 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 463279 numLines: 463279 ebwtTotLen: 29649856 ebwtTotSz: 29649856 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:01:09 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: 00:00:02 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 22237368 Using parameters --bmax 16678026 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 16678026 --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: 00:00:01 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: 00:00:03 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: 00:00:04 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.11187e+07 (target: 16678025) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (16678026) 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 7049423 (Using difference cover) Sorting block time: 00:00:02 Returning block of 7049424 Getting block 2 of 8 Reserving size (16678026) 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 9933166 (Using difference cover) Sorting block time: 00:00:03 Returning block of 9933167 Getting block 3 of 8 Reserving size (16678026) 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 12596354 (Using difference cover) Sorting block time: 00:00:04 Returning block of 12596355 Getting block 4 of 8 Reserving size (16678026) 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: 00:00:02 Sorting block of length 4601089 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4601090 Getting block 5 of 8 Reserving size (16678026) 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: 00:00:02 Sorting block of length 16602437 (Using difference cover) Sorting block time: 00:00:05 Returning block of 16602438 Getting block 6 of 8 Reserving size (16678026) 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: 00:00:02 Sorting block of length 14909661 (Using difference cover) Sorting block time: 00:00:04 Returning block of 14909662 Getting block 7 of 8 Reserving size (16678026) 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 15505757 (Using difference cover) Sorting block time: 00:00:06 Returning block of 15505758 Getting block 8 of 8 Reserving size (16678026) 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 7751581 (Using difference cover) Sorting block time: 00:00:02 Returning block of 7751582 Exited Ebwt loop fchr[A]: 0 fchr[C]: 28922758 fchr[G]: 44882892 fchr[T]: 60810796 fchr[$]: 88949475 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 149399405 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.rev.1.bt2 Wrote 22237376 bytes to secondary EBWT file: ./tophat_out/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 88949475 bwtLen: 88949476 sz: 22237369 bwtSz: 22237369 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5559343 offsSz: 22237372 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 463279 numLines: 463279 ebwtTotLen: 29649856 ebwtTotSz: 29649856 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:01:03