Settings: Output files: "/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K6_08595/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: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K6_08595/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: 2822950 Using parameters --bmax 2117213 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2117213 --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 Avg bucket size: 1.41147e+06 (target: 2117212) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2117213) 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 1750378 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1750379 Getting block 2 of 8 Reserving size (2117213) 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 1141904 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1141905 Getting block 3 of 8 Reserving size (2117213) 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 1832751 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1832752 Getting block 4 of 8 Reserving size (2117213) 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 2080837 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2080838 Getting block 5 of 8 Reserving size (2117213) 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 499608 (Using difference cover) Sorting block time: 00:00:00 Returning block of 499609 Getting block 6 of 8 Reserving size (2117213) 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 1708812 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1708813 Getting block 7 of 8 Reserving size (2117213) 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 488856 (Using difference cover) Sorting block time: 00:00:00 Returning block of 488857 Getting block 8 of 8 Reserving size (2117213) 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 1788647 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1788648 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2803334 fchr[G]: 5641717 fchr[T]: 8484270 fchr[$]: 11291800 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22661268 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K6_08595/tmp/segment_juncs.1.ebwt Wrote 1411480 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K6_08595/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11291800 bwtLen: 11291801 sz: 2822950 bwtSz: 2822951 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 352869 offsSz: 1411476 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 25205 numSides: 50410 numLines: 50410 ebwtTotLen: 3226240 ebwtTotSz: 3226240 reverse: 0 Total time for call to driver() for forward index: 00:00:06 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: 2822950 Using parameters --bmax 2117213 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2117213 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.61311e+06 (target: 2117212) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2117213) 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 1095017 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1095018 Getting block 2 of 7 Reserving size (2117213) 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 1722629 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1722630 Getting block 3 of 7 Reserving size (2117213) 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 2068882 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2068883 Getting block 4 of 7 Reserving size (2117213) 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 1639129 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1639130 Getting block 5 of 7 Reserving size (2117213) 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 1903968 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1903969 Getting block 6 of 7 Reserving size (2117213) 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 1082541 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1082542 Getting block 7 of 7 Reserving size (2117213) 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 1779628 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1779629 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2803334 fchr[G]: 5641717 fchr[T]: 8484270 fchr[$]: 11291800 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22661268 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K6_08595/tmp/segment_juncs.rev.1.ebwt Wrote 1411480 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K6_08595/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11291800 bwtLen: 11291801 sz: 2822950 bwtSz: 2822951 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 352869 offsSz: 1411476 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 25205 numSides: 50410 numLines: 50410 ebwtTotLen: 3226240 ebwtTotSz: 3226240 reverse: 0 Total time for backward call to driver() for mirror index: 00:00:05