Settings: Output files: "IR_Brain_02FC_1/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: IR_Brain_02FC_1/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: 4099055 Using parameters --bmax 3074292 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3074292 --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 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: 1.8218e+06 (target: 3074291) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (3074292) 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 1994619 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1994620 Getting block 2 of 9 Reserving size (3074292) 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 2049338 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2049339 Getting block 3 of 9 Reserving size (3074292) 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 1132271 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1132272 Getting block 4 of 9 Reserving size (3074292) 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 2417178 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2417179 Getting block 5 of 9 Reserving size (3074292) 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 932662 (Using difference cover) Sorting block time: 00:00:01 Returning block of 932663 Getting block 6 of 9 Reserving size (3074292) 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 2231225 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2231226 Getting block 7 of 9 Reserving size (3074292) 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 1012170 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1012171 Getting block 8 of 9 Reserving size (3074292) 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 2629352 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2629353 Getting block 9 of 9 Reserving size (3074292) 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 1997397 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1997398 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3935898 fchr[G]: 8227533 fchr[T]: 12325528 fchr[$]: 16396220 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30923747 bytes to primary EBWT file: IR_Brain_02FC_1/tmp/segment_juncs.1.bt2 Wrote 4099060 bytes to secondary EBWT file: IR_Brain_02FC_1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16396220 bwtLen: 16396221 sz: 4099055 bwtSz: 4099056 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1024764 offsSz: 4099056 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 85397 numLines: 85397 ebwtTotLen: 5465408 ebwtTotSz: 5465408 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:14 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: 4099055 Using parameters --bmax 3074292 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3074292 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.04953e+06 (target: 3074291) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3074292) 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 1453552 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1453553 Getting block 2 of 8 Reserving size (3074292) 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 2329390 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2329391 Getting block 3 of 8 Reserving size (3074292) 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 1395172 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1395173 Getting block 4 of 8 Reserving size (3074292) 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 2277997 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2277998 Getting block 5 of 8 Reserving size (3074292) 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 2920202 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2920203 Getting block 6 of 8 Reserving size (3074292) 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 2741333 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2741334 Getting block 7 of 8 Reserving size (3074292) 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 1926948 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1926949 Getting block 8 of 8 Reserving size (3074292) 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 1351619 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1351620 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3935898 fchr[G]: 8227533 fchr[T]: 12325528 fchr[$]: 16396220 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30923747 bytes to primary EBWT file: IR_Brain_02FC_1/tmp/segment_juncs.rev.1.bt2 Wrote 4099060 bytes to secondary EBWT file: IR_Brain_02FC_1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16396220 bwtLen: 16396221 sz: 4099055 bwtSz: 4099056 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1024764 offsSz: 4099056 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 85397 numLines: 85397 ebwtTotLen: 5465408 ebwtTotSz: 5465408 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:13