Settings: Output files: "MCSpleen18b/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: MCSpleen18b/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: 4515368 Using parameters --bmax 3386526 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3386526 --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 2, 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: 2.00683e+06 (target: 3386525) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (3386526) 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 2119283 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2119284 Getting block 2 of 9 Reserving size (3386526) 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 1671600 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1671601 Getting block 3 of 9 Reserving size (3386526) 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 2351797 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2351798 Getting block 4 of 9 Reserving size (3386526) 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 1506125 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1506126 Getting block 5 of 9 Reserving size (3386526) 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 2459051 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2459052 Getting block 6 of 9 Reserving size (3386526) 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 2047768 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2047769 Getting block 7 of 9 Reserving size (3386526) 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 1703886 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1703887 Getting block 8 of 9 Reserving size (3386526) 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 1735914 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1735915 Getting block 9 of 9 Reserving size (3386526) 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 2466040 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2466041 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4354709 fchr[G]: 9069118 fchr[T]: 13501929 fchr[$]: 18061472 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33749865 bytes to primary EBWT file: MCSpleen18b/tmp/segment_juncs.1.bt2 Wrote 4515376 bytes to secondary EBWT file: MCSpleen18b/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18061472 bwtLen: 18061473 sz: 4515368 bwtSz: 4515369 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1128843 offsSz: 4515372 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 94071 numLines: 94071 ebwtTotLen: 6020544 ebwtTotSz: 6020544 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: 4515368 Using parameters --bmax 3386526 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3386526 --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 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: 2.58021e+06 (target: 3386525) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3386526) 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 2513092 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2513093 Getting block 2 of 7 Reserving size (3386526) 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 3258095 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3258096 Getting block 3 of 7 Reserving size (3386526) 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 2833509 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2833510 Getting block 4 of 7 Reserving size (3386526) 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 3328107 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3328108 Getting block 5 of 7 Reserving size (3386526) 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 1466317 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1466318 Getting block 6 of 7 Reserving size (3386526) 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 2281149 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2281150 Getting block 7 of 7 Reserving size (3386526) 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 2381197 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2381198 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4354709 fchr[G]: 9069118 fchr[T]: 13501929 fchr[$]: 18061472 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33749865 bytes to primary EBWT file: MCSpleen18b/tmp/segment_juncs.rev.1.bt2 Wrote 4515376 bytes to secondary EBWT file: MCSpleen18b/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18061472 bwtLen: 18061473 sz: 4515368 bwtSz: 4515369 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1128843 offsSz: 4515372 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 94071 numLines: 94071 ebwtTotLen: 6020544 ebwtTotSz: 6020544 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:15