Settings: Output files: "/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114P_08592/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_114P_08592/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: 2833812 Using parameters --bmax 2125359 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2125359 --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 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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.61932e+06 (target: 2125358) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2125359) 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 1790665 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1790666 Getting block 2 of 7 Reserving size (2125359) 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 1367994 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1367995 Getting block 3 of 7 Reserving size (2125359) 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 995562 (Using difference cover) Sorting block time: 00:00:00 Returning block of 995563 Getting block 4 of 7 Reserving size (2125359) 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 1507245 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1507246 Getting block 5 of 7 Reserving size (2125359) 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 2008720 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2008721 Getting block 6 of 7 Reserving size (2125359) 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 1781284 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1781285 Getting block 7 of 7 Reserving size (2125359) 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 1883774 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1883775 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2812688 fchr[G]: 5661711 fchr[T]: 8516452 fchr[$]: 11335250 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22732894 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114P_08592/tmp/segment_juncs.1.ebwt Wrote 1416912 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114P_08592/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11335250 bwtLen: 11335251 sz: 2833813 bwtSz: 2833813 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 354227 offsSz: 1416908 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 25302 numSides: 50604 numLines: 50604 ebwtTotLen: 3238656 ebwtTotSz: 3238656 reverse: 0 Total time for call to driver() for forward index: 00:00:05 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: 2833812 Using parameters --bmax 2125359 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2125359 --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 Split 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.41691e+06 (target: 2125358) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2125359) 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 1616277 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1616278 Getting block 2 of 8 Reserving size (2125359) 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 1065336 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1065337 Getting block 3 of 8 Reserving size (2125359) 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 1900166 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1900167 Getting block 4 of 8 Reserving size (2125359) 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 1703475 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1703476 Getting block 5 of 8 Reserving size (2125359) 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 1328998 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1328999 Getting block 6 of 8 Reserving size (2125359) 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 1328441 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1328442 Getting block 7 of 8 Reserving size (2125359) 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 1901016 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1901017 Getting block 8 of 8 Reserving size (2125359) 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 491534 (Using difference cover) Sorting block time: 00:00:00 Returning block of 491535 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2812688 fchr[G]: 5661711 fchr[T]: 8516452 fchr[$]: 11335250 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22732894 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114P_08592/tmp/segment_juncs.rev.1.ebwt Wrote 1416912 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114P_08592/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11335250 bwtLen: 11335251 sz: 2833813 bwtSz: 2833813 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 354227 offsSz: 1416908 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 25302 numSides: 50604 numLines: 50604 ebwtTotLen: 3238656 ebwtTotSz: 3238656 reverse: 0 Total time for backward call to driver() for mirror index: 00:00:05