Settings: Output files: "IR_Liver_131/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_Liver_131/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: 4723693 Using parameters --bmax 3542770 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3542770 --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 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: 2.69925e+06 (target: 3542769) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3542770) 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 1949705 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1949706 Getting block 2 of 7 Reserving size (3542770) 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 3458585 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3458586 Getting block 3 of 7 Reserving size (3542770) 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 2398630 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2398631 Getting block 4 of 7 Reserving size (3542770) 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 2673736 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2673737 Getting block 5 of 7 Reserving size (3542770) 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 3152177 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3152178 Getting block 6 of 7 Reserving size (3542770) 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 3074597 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3074598 Getting block 7 of 7 Reserving size (3542770) 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 2187336 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2187337 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4759412 fchr[G]: 9322537 fchr[T]: 13669940 fchr[$]: 18894772 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 34888830 bytes to primary EBWT file: IR_Liver_131/tmp/segment_juncs.1.bt2 Wrote 4723700 bytes to secondary EBWT file: IR_Liver_131/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18894772 bwtLen: 18894773 sz: 4723693 bwtSz: 4723694 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1180924 offsSz: 4723696 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 98411 numLines: 98411 ebwtTotLen: 6298304 ebwtTotSz: 6298304 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: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4723693 Using parameters --bmax 3542770 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3542770 --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 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 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: 2.69925e+06 (target: 3542769) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3542770) 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 2511482 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2511483 Getting block 2 of 7 Reserving size (3542770) 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 2630142 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2630143 Getting block 3 of 7 Reserving size (3542770) 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 2133518 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2133519 Getting block 4 of 7 Reserving size (3542770) 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 3264629 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3264630 Getting block 5 of 7 Reserving size (3542770) 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 3148594 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3148595 Getting block 6 of 7 Reserving size (3542770) 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 2526615 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2526616 Getting block 7 of 7 Reserving size (3542770) 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 2679786 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2679787 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4759412 fchr[G]: 9322537 fchr[T]: 13669940 fchr[$]: 18894772 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 34888830 bytes to primary EBWT file: IR_Liver_131/tmp/segment_juncs.rev.1.bt2 Wrote 4723700 bytes to secondary EBWT file: IR_Liver_131/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18894772 bwtLen: 18894773 sz: 4723693 bwtSz: 4723694 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1180924 offsSz: 4723696 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 98411 numLines: 98411 ebwtTotLen: 6298304 ebwtTotSz: 6298304 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:28