Settings: Output files: "CB_Brain_tp4a/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_Brain_tp4a/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: 00:00:00 bmax according to bmaxDivN setting: 4285382 Using parameters --bmax 3214037 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3214037 --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 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 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: 2.14269e+06 (target: 3214036) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3214037) 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 1178616 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1178617 Getting block 2 of 8 Reserving size (3214037) 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 2845883 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2845884 Getting block 3 of 8 Reserving size (3214037) 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 2803508 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2803509 Getting block 4 of 8 Reserving size (3214037) 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 1975695 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1975696 Getting block 5 of 8 Reserving size (3214037) 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 1525813 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1525814 Getting block 6 of 8 Reserving size (3214037) 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 2477042 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2477043 Getting block 7 of 8 Reserving size (3214037) 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 2516130 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2516131 Getting block 8 of 8 Reserving size (3214037) 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 1818837 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1818838 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4110853 fchr[G]: 8581655 fchr[T]: 12848160 fchr[$]: 17141531 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32136937 bytes to primary EBWT file: CB_Brain_tp4a/tmp/segment_juncs.1.bt2 Wrote 4285388 bytes to secondary EBWT file: CB_Brain_tp4a/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17141531 bwtLen: 17141532 sz: 4285383 bwtSz: 4285383 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1071346 offsSz: 4285384 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 89279 numLines: 89279 ebwtTotLen: 5713856 ebwtTotSz: 5713856 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:13 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: 4285382 Using parameters --bmax 3214037 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3214037 --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 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 Split 2, merged 0; 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 2, 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: 2.14269e+06 (target: 3214036) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3214037) 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 3171696 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3171697 Getting block 2 of 8 Reserving size (3214037) 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 1621086 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1621087 Getting block 3 of 8 Reserving size (3214037) 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 1962594 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1962595 Getting block 4 of 8 Reserving size (3214037) 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 2644604 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2644605 Getting block 5 of 8 Reserving size (3214037) 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 2375150 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2375151 Getting block 6 of 8 Reserving size (3214037) 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 1090491 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1090492 Getting block 7 of 8 Reserving size (3214037) 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 3173909 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3173910 Getting block 8 of 8 Reserving size (3214037) 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 1101994 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1101995 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4110853 fchr[G]: 8581655 fchr[T]: 12848160 fchr[$]: 17141531 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 32136937 bytes to primary EBWT file: CB_Brain_tp4a/tmp/segment_juncs.rev.1.bt2 Wrote 4285388 bytes to secondary EBWT file: CB_Brain_tp4a/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17141531 bwtLen: 17141532 sz: 4285383 bwtSz: 4285383 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1071346 offsSz: 4285384 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 89279 numLines: 89279 ebwtTotLen: 5713856 ebwtTotSz: 5713856 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:14