Settings: Output files: "CB_Thyroid_tp121/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_tp121/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: 3916185 Using parameters --bmax 2937139 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2937139 --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 1, 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 Avg bucket size: 2.23782e+06 (target: 2937138) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2937139) 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 1907203 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1907204 Getting block 2 of 7 Reserving size (2937139) 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 2835204 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2835205 Getting block 3 of 7 Reserving size (2937139) 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 2910679 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2910680 Getting block 4 of 7 Reserving size (2937139) 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 2228482 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2228483 Getting block 5 of 7 Reserving size (2937139) 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 2140036 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2140037 Getting block 6 of 7 Reserving size (2937139) 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 1460392 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1460393 Getting block 7 of 7 Reserving size (2937139) 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 2182738 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2182739 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3709067 fchr[G]: 7848032 fchr[T]: 11786258 fchr[$]: 15664740 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 29772401 bytes to primary EBWT file: CB_Thyroid_tp121/tmp/segment_juncs.1.bt2 Wrote 3916192 bytes to secondary EBWT file: CB_Thyroid_tp121/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15664740 bwtLen: 15664741 sz: 3916185 bwtSz: 3916186 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 979047 offsSz: 3916188 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 81588 numLines: 81588 ebwtTotLen: 5221632 ebwtTotSz: 5221632 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:15 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: 3916185 Using parameters --bmax 2937139 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2937139 --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: 00:00:00 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 Split 1, 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 Avg bucket size: 1.95809e+06 (target: 2937138) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2937139) 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 2408242 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2408243 Getting block 2 of 8 Reserving size (2937139) 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 2811747 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2811748 Getting block 3 of 8 Reserving size (2937139) 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 2739743 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2739744 Getting block 4 of 8 Reserving size (2937139) 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 1185523 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1185524 Getting block 5 of 8 Reserving size (2937139) 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 2040318 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2040319 Getting block 6 of 8 Reserving size (2937139) 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 1384606 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1384607 Getting block 7 of 8 Reserving size (2937139) 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 2109342 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2109343 Getting block 8 of 8 Reserving size (2937139) 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 985212 (Using difference cover) Sorting block time: 00:00:00 Returning block of 985213 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3709067 fchr[G]: 7848032 fchr[T]: 11786258 fchr[$]: 15664740 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 29772401 bytes to primary EBWT file: CB_Thyroid_tp121/tmp/segment_juncs.rev.1.bt2 Wrote 3916192 bytes to secondary EBWT file: CB_Thyroid_tp121/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 15664740 bwtLen: 15664741 sz: 3916185 bwtSz: 3916186 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 979047 offsSz: 3916188 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 81588 numLines: 81588 ebwtTotLen: 5221632 ebwtTotSz: 5221632 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:16