Settings: Output files: "IRTestis02FC_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: IRTestis02FC_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: 00:00:01 bmax according to bmaxDivN setting: 6413155 Using parameters --bmax 4809867 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4809867 --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 Avg bucket size: 3.20658e+06 (target: 4809866) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4809867) 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 1040763 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1040764 Getting block 2 of 8 Reserving size (4809867) 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 4339380 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4339381 Getting block 3 of 8 Reserving size (4809867) 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 2070354 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2070355 Getting block 4 of 8 Reserving size (4809867) 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 4099289 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4099290 Getting block 5 of 8 Reserving size (4809867) 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 3422916 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3422917 Getting block 6 of 8 Reserving size (4809867) 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 3329298 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3329299 Getting block 7 of 8 Reserving size (4809867) 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 2818027 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2818028 Getting block 8 of 8 Reserving size (4809867) 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 4532589 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4532590 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6318786 fchr[G]: 12874971 fchr[T]: 19190853 fchr[$]: 25652623 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 45970479 bytes to primary EBWT file: IRTestis02FC_1/tmp/segment_juncs.1.bt2 Wrote 6413160 bytes to secondary EBWT file: IRTestis02FC_1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 25652623 bwtLen: 25652624 sz: 6413156 bwtSz: 6413156 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1603289 offsSz: 6413156 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 133608 numLines: 133608 ebwtTotLen: 8550912 ebwtTotSz: 8550912 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:26 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: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 6413155 Using parameters --bmax 4809867 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4809867 --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 7; iterating... 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: 3.66466e+06 (target: 4809866) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4809867) 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 1157582 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1157583 Getting block 2 of 7 Reserving size (4809867) 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 4368676 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4368677 Getting block 3 of 7 Reserving size (4809867) 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 4662565 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4662566 Getting block 4 of 7 Reserving size (4809867) 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 4580303 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4580304 Getting block 5 of 7 Reserving size (4809867) 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 4188896 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4188897 Getting block 6 of 7 Reserving size (4809867) 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 2301527 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2301528 Getting block 7 of 7 Reserving size (4809867) 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 4393068 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4393069 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6318786 fchr[G]: 12874971 fchr[T]: 19190853 fchr[$]: 25652623 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 45970479 bytes to primary EBWT file: IRTestis02FC_1/tmp/segment_juncs.rev.1.bt2 Wrote 6413160 bytes to secondary EBWT file: IRTestis02FC_1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 25652623 bwtLen: 25652624 sz: 6413156 bwtSz: 6413156 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1603289 offsSz: 6413156 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 133608 numLines: 133608 ebwtTotLen: 8550912 ebwtTotSz: 8550912 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:26