Settings: Output files: "IRLung131/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: IRLung131/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: 00:00:01 bmax according to bmaxDivN setting: 4799272 Using parameters --bmax 3599454 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3599454 --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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; 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: 2.39964e+06 (target: 3599453) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3599454) 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 2953333 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2953334 Getting block 2 of 8 Reserving size (3599454) 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 3069062 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3069063 Getting block 3 of 8 Reserving size (3599454) 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 1594727 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1594728 Getting block 4 of 8 Reserving size (3599454) 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 2384295 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2384296 Getting block 5 of 8 Reserving size (3599454) 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 2502751 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2502752 Getting block 6 of 8 Reserving size (3599454) 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 2373078 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2373079 Getting block 7 of 8 Reserving size (3599454) 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 2423479 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2423480 Getting block 8 of 8 Reserving size (3599454) 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 1896359 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1896360 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4647614 fchr[G]: 9652924 fchr[T]: 14379127 fchr[$]: 19197091 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 35500344 bytes to primary EBWT file: IRLung131/tmp/segment_juncs.1.bt2 Wrote 4799280 bytes to secondary EBWT file: IRLung131/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19197091 bwtLen: 19197092 sz: 4799273 bwtSz: 4799273 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1199819 offsSz: 4799276 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 99985 numLines: 99985 ebwtTotLen: 6399040 ebwtTotSz: 6399040 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:17 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: 4799272 Using parameters --bmax 3599454 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3599454 --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: 00:00:02 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: 00:00:01 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: 00:00:01 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.39964e+06 (target: 3599453) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3599454) 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 2212834 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2212835 Getting block 2 of 8 Reserving size (3599454) 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 2545776 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2545777 Getting block 3 of 8 Reserving size (3599454) 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 3101182 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3101183 Getting block 4 of 8 Reserving size (3599454) 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 510437 (Using difference cover) Sorting block time: 00:00:00 Returning block of 510438 Getting block 5 of 8 Reserving size (3599454) 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 3157968 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3157969 Getting block 6 of 8 Reserving size (3599454) 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 2037228 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2037229 Getting block 7 of 8 Reserving size (3599454) 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 3594097 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3594098 Getting block 8 of 8 Reserving size (3599454) 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 2037562 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2037563 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4647614 fchr[G]: 9652924 fchr[T]: 14379127 fchr[$]: 19197091 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 35500344 bytes to primary EBWT file: IRLung131/tmp/segment_juncs.rev.1.bt2 Wrote 4799280 bytes to secondary EBWT file: IRLung131/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19197091 bwtLen: 19197092 sz: 4799273 bwtSz: 4799273 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1199819 offsSz: 4799276 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 99985 numLines: 99985 ebwtTotLen: 6399040 ebwtTotSz: 6399040 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:18