Settings: Output files: "CB_Liver_tp4a/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_Liver_tp4a/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: 5514132 Using parameters --bmax 4135599 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4135599 --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: 00:00:01 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 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 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: 3.15093e+06 (target: 4135598) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4135599) 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 3647811 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3647812 Getting block 2 of 7 Reserving size (4135599) 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 3992427 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3992428 Getting block 3 of 7 Reserving size (4135599) 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 661888 (Using difference cover) Sorting block time: 00:00:01 Returning block of 661889 Getting block 4 of 7 Reserving size (4135599) 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 4065195 (Using difference cover) Sorting block time: 00:00:05 Returning block of 4065196 Getting block 5 of 7 Reserving size (4135599) 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 3668261 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3668262 Getting block 6 of 7 Reserving size (4135599) 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 2312550 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2312551 Getting block 7 of 7 Reserving size (4135599) 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 3708390 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3708391 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5577376 fchr[G]: 10869179 fchr[T]: 15942532 fchr[$]: 22056528 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 40016528 bytes to primary EBWT file: CB_Liver_tp4a/tmp/segment_juncs.1.bt2 Wrote 5514140 bytes to secondary EBWT file: CB_Liver_tp4a/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 22056528 bwtLen: 22056529 sz: 5514132 bwtSz: 5514133 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1378534 offsSz: 5514136 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 114878 numLines: 114878 ebwtTotLen: 7352192 ebwtTotSz: 7352192 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:38 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: 5514132 Using parameters --bmax 4135599 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4135599 --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: 00:00:02 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: 00:00:00 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: 3.15093e+06 (target: 4135598) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4135599) 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 3734935 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3734936 Getting block 2 of 7 Reserving size (4135599) 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 3679984 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3679985 Getting block 3 of 7 Reserving size (4135599) 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 1494462 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1494463 Getting block 4 of 7 Reserving size (4135599) 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 3538909 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3538910 Getting block 5 of 7 Reserving size (4135599) 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 2374197 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2374198 Getting block 6 of 7 Reserving size (4135599) 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 3757456 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3757457 Getting block 7 of 7 Reserving size (4135599) 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 3476579 (Using difference cover) Sorting block time: 00:00:05 Returning block of 3476580 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5577376 fchr[G]: 10869179 fchr[T]: 15942532 fchr[$]: 22056528 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 40016528 bytes to primary EBWT file: CB_Liver_tp4a/tmp/segment_juncs.rev.1.bt2 Wrote 5514140 bytes to secondary EBWT file: CB_Liver_tp4a/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 22056528 bwtLen: 22056529 sz: 5514132 bwtSz: 5514133 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1378534 offsSz: 5514136 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 114878 numLines: 114878 ebwtTotLen: 7352192 ebwtTotSz: 7352192 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:37