Settings: Output files: "IR_Kidney_07F1C1/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_Kidney_07F1C1/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: 4002309 Using parameters --bmax 3001732 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3001732 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.28703e+06 (target: 3001731) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3001732) 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 2618743 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2618744 Getting block 2 of 7 Reserving size (3001732) 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 1982253 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1982254 Getting block 3 of 7 Reserving size (3001732) 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 2383237 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2383238 Getting block 4 of 7 Reserving size (3001732) 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 2028651 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2028652 Getting block 5 of 7 Reserving size (3001732) 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 1861262 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1861263 Getting block 6 of 7 Reserving size (3001732) 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 2360430 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2360431 Getting block 7 of 7 Reserving size (3001732) 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 2774654 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2774655 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3857842 fchr[G]: 8009150 fchr[T]: 11977102 fchr[$]: 16009236 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30309350 bytes to primary EBWT file: IR_Kidney_07F1C1/tmp/segment_juncs.1.bt2 Wrote 4002316 bytes to secondary EBWT file: IR_Kidney_07F1C1/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16009236 bwtLen: 16009237 sz: 4002309 bwtSz: 4002310 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1000578 offsSz: 4002312 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 83382 numLines: 83382 ebwtTotLen: 5336448 ebwtTotSz: 5336448 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:12 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4002309 Using parameters --bmax 3001732 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3001732 --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 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 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.00115e+06 (target: 3001731) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3001732) 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 1902244 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1902245 Getting block 2 of 8 Reserving size (3001732) 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 1705488 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1705489 Getting block 3 of 8 Reserving size (3001732) 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 2375897 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2375898 Getting block 4 of 8 Reserving size (3001732) 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 2076253 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2076254 Getting block 5 of 8 Reserving size (3001732) 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 1936739 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1936740 Getting block 6 of 8 Reserving size (3001732) 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 2181322 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2181323 Getting block 7 of 8 Reserving size (3001732) 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 1210719 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1210720 Getting block 8 of 8 Reserving size (3001732) 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 2620567 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2620568 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3857842 fchr[G]: 8009150 fchr[T]: 11977102 fchr[$]: 16009236 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 30309350 bytes to primary EBWT file: IR_Kidney_07F1C1/tmp/segment_juncs.rev.1.bt2 Wrote 4002316 bytes to secondary EBWT file: IR_Kidney_07F1C1/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16009236 bwtLen: 16009237 sz: 4002309 bwtSz: 4002310 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1000578 offsSz: 4002312 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 83382 numLines: 83382 ebwtTotLen: 5336448 ebwtTotSz: 5336448 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:12