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: 00:00:00 bmax according to bmaxDivN setting: 5091747 Using parameters --bmax 3818811 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3818811 --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: 00:00:01 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 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.90957e+06 (target: 3818810) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3818811) 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 3604236 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3604237 Getting block 2 of 7 Reserving size (3818811) 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 2643247 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2643248 Getting block 3 of 7 Reserving size (3818811) 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 3231437 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3231438 Getting block 4 of 7 Reserving size (3818811) 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 3517162 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3517163 Getting block 5 of 7 Reserving size (3818811) 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 2839744 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2839745 Getting block 6 of 7 Reserving size (3818811) 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 2710404 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2710405 Getting block 7 of 7 Reserving size (3818811) 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 1820754 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1820755 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5888139 fchr[G]: 10262772 fchr[T]: 14501271 fchr[$]: 20366990 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 42068217 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.1.bt2 Wrote 5091752 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: 20366990 bwtLen: 20366991 sz: 5091748 bwtSz: 5091748 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1272937 offsSz: 5091748 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 106079 numLines: 106079 ebwtTotLen: 6789056 ebwtTotSz: 6789056 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:16 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: 5091747 Using parameters --bmax 3818811 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3818811 --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: 00:00:01 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: 2.54587e+06 (target: 3818810) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3818811) 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 2530158 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2530159 Getting block 2 of 8 Reserving size (3818811) 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 3742124 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3742125 Getting block 3 of 8 Reserving size (3818811) 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 2604893 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2604894 Getting block 4 of 8 Reserving size (3818811) 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 2865929 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2865930 Getting block 5 of 8 Reserving size (3818811) 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 2308914 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2308915 Getting block 6 of 8 Reserving size (3818811) 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 2339942 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2339943 Getting block 7 of 8 Reserving size (3818811) 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 2911735 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2911736 Getting block 8 of 8 Reserving size (3818811) 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 1063288 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1063289 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5888139 fchr[G]: 10262772 fchr[T]: 14501271 fchr[$]: 20366990 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 42068217 bytes to primary EBWT file: ./tophat_out/tmp/segment_juncs.rev.1.bt2 Wrote 5091752 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: 20366990 bwtLen: 20366991 sz: 5091748 bwtSz: 5091748 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1272937 offsSz: 5091748 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 106079 numLines: 106079 ebwtTotLen: 6789056 ebwtTotSz: 6789056 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:15