Settings: Output files: "Po_0//tmp/segment_juncs.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) 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: Po_0//tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:08 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:07 bmax according to bmaxDivN setting: 32415974 Using parameters --bmax 24311981 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 24311981 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:05 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: 00:00:01 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: 00:00:11 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: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.85234e+07 (target: 24311980) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (24311981) 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: 00:00:02 Sorting block of length 24260741 (Using difference cover) Sorting block time: 00:00:17 Returning block of 24260742 Getting block 2 of 7 Reserving size (24311981) 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: 00:00:04 Sorting block of length 22067532 (Using difference cover) Sorting block time: 00:00:24 Returning block of 22067533 Getting block 3 of 7 Reserving size (24311981) 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: 00:00:06 Sorting block of length 21317247 (Using difference cover) Sorting block time: 00:00:24 Returning block of 21317248 Getting block 4 of 7 Reserving size (24311981) 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: 00:00:05 Sorting block of length 14929726 (Using difference cover) Sorting block time: 00:00:13 Returning block of 14929727 Getting block 5 of 7 Reserving size (24311981) 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: 00:00:07 Sorting block of length 19541003 (Using difference cover) Sorting block time: 00:00:18 Returning block of 19541004 Getting block 6 of 7 Reserving size (24311981) 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: 00:00:06 Sorting block of length 23463156 (Using difference cover) Sorting block time: 00:00:26 Returning block of 23463157 Getting block 7 of 7 Reserving size (24311981) 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: 00:00:04 Sorting block of length 4084488 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4084489 Exited Ebwt loop fchr[A]: 0 fchr[C]: 39707037 fchr[G]: 64793742 fchr[T]: 90033053 fchr[$]: 129663899 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 229650606 bytes to primary EBWT file: Po_0//tmp/segment_juncs.1.ebwt Wrote 16207992 bytes to secondary EBWT file: Po_0//tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 129663899 bwtLen: 129663900 sz: 32415975 bwtSz: 32415975 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4051997 offsSz: 16207988 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 289429 numSides: 578858 numLines: 578858 ebwtTotLen: 37046912 ebwtTotSz: 37046912 reverse: 0 Total time for call to driver() for forward index: 00:04:03 Reading reference sizes Time reading reference sizes: 00:00:08 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:11 bmax according to bmaxDivN setting: 32415974 Using parameters --bmax 24311981 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 24311981 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:08 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: 00:00:03 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: 00:00:15 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: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.44071e+07 (target: 24311980) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (24311981) 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: 00:00:03 Sorting block of length 4082942 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4082943 Getting block 2 of 9 Reserving size (24311981) 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: 00:00:05 Sorting block of length 23024428 (Using difference cover) Sorting block time: 00:00:27 Returning block of 23024429 Getting block 3 of 9 Reserving size (24311981) 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: 00:00:04 Sorting block of length 14477339 (Using difference cover) Sorting block time: 00:00:13 Returning block of 14477340 Getting block 4 of 9 Reserving size (24311981) 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: 00:00:04 Sorting block of length 21275358 (Using difference cover) Sorting block time: 00:00:24 Returning block of 21275359 Getting block 5 of 9 Reserving size (24311981) 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: 00:00:06 Sorting block of length 4081976 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4081977 Getting block 6 of 9 Reserving size (24311981) 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: 00:00:05 Sorting block of length 21337330 (Using difference cover) Sorting block time: 00:00:25 Returning block of 21337331 Getting block 7 of 9 Reserving size (24311981) 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: 00:00:06 Sorting block of length 14491482 (Using difference cover) Sorting block time: 00:00:14 Returning block of 14491483 Getting block 8 of 9 Reserving size (24311981) 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: 00:00:06 Sorting block of length 16658702 (Using difference cover) Sorting block time: 00:00:19 Returning block of 16658703 Getting block 9 of 9 Reserving size (24311981) 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: 00:00:04 Sorting block of length 10234334 (Using difference cover) Sorting block time: 00:00:13 Returning block of 10234335 Exited Ebwt loop fchr[A]: 0 fchr[C]: 39707037 fchr[G]: 64793742 fchr[T]: 90033053 fchr[$]: 129663899 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 229650606 bytes to primary EBWT file: Po_0//tmp/segment_juncs.rev.1.ebwt Wrote 16207992 bytes to secondary EBWT file: Po_0//tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 129663899 bwtLen: 129663900 sz: 32415975 bwtSz: 32415975 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4051997 offsSz: 16207988 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 289429 numSides: 578858 numLines: 578858 ebwtTotLen: 37046912 ebwtTotSz: 37046912 reverse: 0 Total time for backward call to driver() for mirror index: 00:04:56