Settings: Output files: "IRLung08F1_A/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: IRLung08F1_A/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: 00:00:00 bmax according to bmaxDivN setting: 5142186 Using parameters --bmax 3856640 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3856640 --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 5; 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: 2.28542e+06 (target: 3856639) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (3856640) 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 1918326 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1918327 Getting block 2 of 9 Reserving size (3856640) 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 2728271 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2728272 Getting block 3 of 9 Reserving size (3856640) 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 1878383 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1878384 Getting block 4 of 9 Reserving size (3856640) 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 2643331 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2643332 Getting block 5 of 9 Reserving size (3856640) 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 1680699 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1680700 Getting block 6 of 9 Reserving size (3856640) 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 3334873 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3334874 Getting block 7 of 9 Reserving size (3856640) 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 950192 (Using difference cover) Sorting block time: 00:00:01 Returning block of 950193 Getting block 8 of 9 Reserving size (3856640) 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 3071068 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3071069 Getting block 9 of 9 Reserving size (3856640) 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 2363596 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2363597 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4947875 fchr[G]: 10373100 fchr[T]: 15449374 fchr[$]: 20568747 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37758691 bytes to primary EBWT file: IRLung08F1_A/tmp/segment_juncs.1.bt2 Wrote 5142192 bytes to secondary EBWT file: IRLung08F1_A/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20568747 bwtLen: 20568748 sz: 5142187 bwtSz: 5142187 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1285547 offsSz: 5142188 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 107129 numLines: 107129 ebwtTotLen: 6856256 ebwtTotSz: 6856256 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:20 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: 5142186 Using parameters --bmax 3856640 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3856640 --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 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 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 1; iterating... Avg bucket size: 2.57109e+06 (target: 3856639) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3856640) 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 2064947 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2064948 Getting block 2 of 8 Reserving size (3856640) 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 3200967 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3200968 Getting block 3 of 8 Reserving size (3856640) 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 967485 (Using difference cover) Sorting block time: 00:00:01 Returning block of 967486 Getting block 4 of 8 Reserving size (3856640) 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 2839511 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2839512 Getting block 5 of 8 Reserving size (3856640) 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 3720244 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3720245 Getting block 6 of 8 Reserving size (3856640) 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 3194581 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3194582 Getting block 7 of 8 Reserving size (3856640) 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 2202374 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2202375 Getting block 8 of 8 Reserving size (3856640) 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 2378631 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2378632 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4947875 fchr[G]: 10373100 fchr[T]: 15449374 fchr[$]: 20568747 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37758691 bytes to primary EBWT file: IRLung08F1_A/tmp/segment_juncs.rev.1.bt2 Wrote 5142192 bytes to secondary EBWT file: IRLung08F1_A/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20568747 bwtLen: 20568748 sz: 5142187 bwtSz: 5142187 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1285547 offsSz: 5142188 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 107129 numLines: 107129 ebwtTotLen: 6856256 ebwtTotSz: 6856256 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:21