Settings: Output files: "CB_Thyroid_tp51/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: CB_Thyroid_tp51/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: 4338060 Using parameters --bmax 3253545 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3253545 --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 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: 2.16903e+06 (target: 3253544) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3253545) 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 2031967 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2031968 Getting block 2 of 8 Reserving size (3253545) 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 1704359 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1704360 Getting block 3 of 8 Reserving size (3253545) 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 2266021 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2266022 Getting block 4 of 8 Reserving size (3253545) 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 1767075 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1767076 Getting block 5 of 8 Reserving size (3253545) 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 3111235 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3111236 Getting block 6 of 8 Reserving size (3253545) 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 1732246 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1732247 Getting block 7 of 8 Reserving size (3253545) 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 3056534 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3056535 Getting block 8 of 8 Reserving size (3253545) 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 1682798 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1682799 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4099020 fchr[G]: 8709738 fchr[T]: 13063096 fchr[$]: 17352242 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32520054 bytes to primary EBWT file: CB_Thyroid_tp51/tmp/segment_juncs.1.bt2 Wrote 4338068 bytes to secondary EBWT file: CB_Thyroid_tp51/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17352242 bwtLen: 17352243 sz: 4338061 bwtSz: 4338061 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1084516 offsSz: 4338064 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 90377 numLines: 90377 ebwtTotLen: 5784128 ebwtTotSz: 5784128 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:19 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: 4338060 Using parameters --bmax 3253545 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3253545 --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: 2.16903e+06 (target: 3253544) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3253545) 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 1808629 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1808630 Getting block 2 of 8 Reserving size (3253545) 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 1714500 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1714501 Getting block 3 of 8 Reserving size (3253545) 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 2171009 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2171010 Getting block 4 of 8 Reserving size (3253545) 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 3060563 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3060564 Getting block 5 of 8 Reserving size (3253545) 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 2151687 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2151688 Getting block 6 of 8 Reserving size (3253545) 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 2013461 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2013462 Getting block 7 of 8 Reserving size (3253545) 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 2781485 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2781486 Getting block 8 of 8 Reserving size (3253545) 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 1650901 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1650902 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4099020 fchr[G]: 8709738 fchr[T]: 13063096 fchr[$]: 17352242 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32520054 bytes to primary EBWT file: CB_Thyroid_tp51/tmp/segment_juncs.rev.1.bt2 Wrote 4338068 bytes to secondary EBWT file: CB_Thyroid_tp51/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17352242 bwtLen: 17352243 sz: 4338061 bwtSz: 4338061 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1084516 offsSz: 4338064 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 90377 numLines: 90377 ebwtTotLen: 5784128 ebwtTotSz: 5784128 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:18