Settings: Output files: "IRThyroid08F1_A/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: IRThyroid08F1_A/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: 4414083 Using parameters --bmax 3310563 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3310563 --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 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: 2.52233e+06 (target: 3310562) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3310563) 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 2777981 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2777982 Getting block 2 of 7 Reserving size (3310563) 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 3280669 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3280670 Getting block 3 of 7 Reserving size (3310563) 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 2062747 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2062748 Getting block 4 of 7 Reserving size (3310563) 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 1897267 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1897268 Getting block 5 of 7 Reserving size (3310563) 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 2465189 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2465190 Getting block 6 of 7 Reserving size (3310563) 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 3163990 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3163991 Getting block 7 of 7 Reserving size (3310563) 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 2008485 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2008486 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4168203 fchr[G]: 8950697 fchr[T]: 13336602 fchr[$]: 17656334 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33017828 bytes to primary EBWT file: IRThyroid08F1_A/tmp/segment_juncs.1.bt2 Wrote 4414088 bytes to secondary EBWT file: IRThyroid08F1_A/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17656334 bwtLen: 17656335 sz: 4414084 bwtSz: 4414084 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1103521 offsSz: 4414084 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 91961 numLines: 91961 ebwtTotLen: 5885504 ebwtTotSz: 5885504 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:18 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4414083 Using parameters --bmax 3310563 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3310563 --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: 2.52233e+06 (target: 3310562) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3310563) 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 3185458 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3185459 Getting block 2 of 7 Reserving size (3310563) 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 3293752 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3293753 Getting block 3 of 7 Reserving size (3310563) 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 1063709 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1063710 Getting block 4 of 7 Reserving size (3310563) 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 2529178 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2529179 Getting block 5 of 7 Reserving size (3310563) 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 3270120 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3270121 Getting block 6 of 7 Reserving size (3310563) 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 2967555 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2967556 Getting block 7 of 7 Reserving size (3310563) 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 1346556 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1346557 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4168203 fchr[G]: 8950697 fchr[T]: 13336602 fchr[$]: 17656334 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33017828 bytes to primary EBWT file: IRThyroid08F1_A/tmp/segment_juncs.rev.1.bt2 Wrote 4414088 bytes to secondary EBWT file: IRThyroid08F1_A/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17656334 bwtLen: 17656335 sz: 4414084 bwtSz: 4414084 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1103521 offsSz: 4414084 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 91961 numLines: 91961 ebwtTotLen: 5885504 ebwtTotSz: 5885504 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:19