Settings: Output files: "CB_Spleen_tp3a2/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_Spleen_tp3a2/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: 5099224 Using parameters --bmax 3824418 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3824418 --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 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: 2.54961e+06 (target: 3824417) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3824418) 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 2981436 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2981437 Getting block 2 of 8 Reserving size (3824418) 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 1701369 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1701370 Getting block 3 of 8 Reserving size (3824418) 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 3616948 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3616949 Getting block 4 of 8 Reserving size (3824418) 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 708890 (Using difference cover) Sorting block time: 00:00:01 Returning block of 708891 Getting block 5 of 8 Reserving size (3824418) 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 3311109 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3311110 Getting block 6 of 8 Reserving size (3824418) 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 3315322 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3315323 Getting block 7 of 8 Reserving size (3824418) 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 2436301 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2436302 Getting block 8 of 8 Reserving size (3824418) 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 2325514 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2325515 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4898639 fchr[G]: 10266622 fchr[T]: 15304296 fchr[$]: 20396896 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37576556 bytes to primary EBWT file: CB_Spleen_tp3a2/tmp/segment_juncs.1.bt2 Wrote 5099232 bytes to secondary EBWT file: CB_Spleen_tp3a2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20396896 bwtLen: 20396897 sz: 5099224 bwtSz: 5099225 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1274807 offsSz: 5099228 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 106234 numLines: 106234 ebwtTotLen: 6798976 ebwtTotSz: 6798976 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:19 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: 5099224 Using parameters --bmax 3824418 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3824418 --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 2, 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 Avg bucket size: 2.54961e+06 (target: 3824417) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3824418) 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 455947 (Using difference cover) Sorting block time: 00:00:00 Returning block of 455948 Getting block 2 of 8 Reserving size (3824418) 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 3549835 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3549836 Getting block 3 of 8 Reserving size (3824418) 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 2724958 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2724959 Getting block 4 of 8 Reserving size (3824418) 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 2639968 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2639969 Getting block 5 of 8 Reserving size (3824418) 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 1215777 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1215778 Getting block 6 of 8 Reserving size (3824418) 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 3579904 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3579905 Getting block 7 of 8 Reserving size (3824418) 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 3772126 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3772127 Getting block 8 of 8 Reserving size (3824418) 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 2458374 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2458375 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4898639 fchr[G]: 10266622 fchr[T]: 15304296 fchr[$]: 20396896 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37576556 bytes to primary EBWT file: CB_Spleen_tp3a2/tmp/segment_juncs.rev.1.bt2 Wrote 5099232 bytes to secondary EBWT file: CB_Spleen_tp3a2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 20396896 bwtLen: 20396897 sz: 5099224 bwtSz: 5099225 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1274807 offsSz: 5099228 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 106234 numLines: 106234 ebwtTotLen: 6798976 ebwtTotSz: 6798976 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:19