Settings: Output files: "MCSpleenB2C/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: MCSpleenB2C/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: 5491769 Using parameters --bmax 4118827 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4118827 --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 Avg bucket size: 2.74588e+06 (target: 4118826) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4118827) 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 1630857 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1630858 Getting block 2 of 8 Reserving size (4118827) 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 3854880 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3854881 Getting block 3 of 8 Reserving size (4118827) 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 3233713 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3233714 Getting block 4 of 8 Reserving size (4118827) 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 2533793 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2533794 Getting block 5 of 8 Reserving size (4118827) 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 2336512 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2336513 Getting block 6 of 8 Reserving size (4118827) 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 3232561 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3232562 Getting block 7 of 8 Reserving size (4118827) 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 3253679 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3253680 Getting block 8 of 8 Reserving size (4118827) 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 1891076 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1891077 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5318205 fchr[G]: 11106470 fchr[T]: 16450567 fchr[$]: 21967078 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 40132706 bytes to primary EBWT file: MCSpleenB2C/tmp/segment_juncs.1.bt2 Wrote 5491776 bytes to secondary EBWT file: MCSpleenB2C/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21967078 bwtLen: 21967079 sz: 5491770 bwtSz: 5491770 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1372943 offsSz: 5491772 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 114412 numLines: 114412 ebwtTotLen: 7322368 ebwtTotSz: 7322368 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:21 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: 5491769 Using parameters --bmax 4118827 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4118827 --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 1, merged 5; 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: 2.74588e+06 (target: 4118826) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4118827) 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 3156064 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3156065 Getting block 2 of 8 Reserving size (4118827) 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 3649981 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3649982 Getting block 3 of 8 Reserving size (4118827) 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 2411455 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2411456 Getting block 4 of 8 Reserving size (4118827) 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 2451199 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2451200 Getting block 5 of 8 Reserving size (4118827) 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 3332460 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3332461 Getting block 6 of 8 Reserving size (4118827) 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 2673892 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2673893 Getting block 7 of 8 Reserving size (4118827) 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 3700229 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3700230 Getting block 8 of 8 Reserving size (4118827) 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 591791 (Using difference cover) Sorting block time: 00:00:00 Returning block of 591792 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5318205 fchr[G]: 11106470 fchr[T]: 16450567 fchr[$]: 21967078 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 40132706 bytes to primary EBWT file: MCSpleenB2C/tmp/segment_juncs.rev.1.bt2 Wrote 5491776 bytes to secondary EBWT file: MCSpleenB2C/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 21967078 bwtLen: 21967079 sz: 5491770 bwtSz: 5491770 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1372943 offsSz: 5491772 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 114412 numLines: 114412 ebwtTotLen: 7322368 ebwtTotSz: 7322368 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:22