Settings: Output files: "/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEP_08586/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_PrEP_08586/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: 00:00:00 bmax according to bmaxDivN setting: 2839287 Using parameters --bmax 2129466 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2129466 --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 Split 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.41964e+06 (target: 2129465) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2129466) 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 977304 (Using difference cover) Sorting block time: 00:00:01 Returning block of 977305 Getting block 2 of 8 Reserving size (2129466) 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 1627219 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1627220 Getting block 3 of 8 Reserving size (2129466) 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 1452128 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1452129 Getting block 4 of 8 Reserving size (2129466) 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 1985416 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1985417 Getting block 5 of 8 Reserving size (2129466) 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 993650 (Using difference cover) Sorting block time: 00:00:00 Returning block of 993651 Getting block 6 of 8 Reserving size (2129466) 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 1623822 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1623823 Getting block 7 of 8 Reserving size (2129466) 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 1124871 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1124872 Getting block 8 of 8 Reserving size (2129466) 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 1572733 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1572734 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2817853 fchr[G]: 5673174 fchr[T]: 8532156 fchr[$]: 11357150 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22768474 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEP_08586/tmp/segment_juncs.1.ebwt Wrote 1419648 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEP_08586/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11357150 bwtLen: 11357151 sz: 2839288 bwtSz: 2839288 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 354911 offsSz: 1419644 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 25351 numSides: 50702 numLines: 50702 ebwtTotLen: 3244928 ebwtTotSz: 3244928 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: 00:00:00 bmax according to bmaxDivN setting: 2839287 Using parameters --bmax 2129466 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2129466 --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 Split 2, merged 6; 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: 1.62245e+06 (target: 2129465) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2129466) 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 1365628 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1365629 Getting block 2 of 7 Reserving size (2129466) 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 1870554 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1870555 Getting block 3 of 7 Reserving size (2129466) 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 1614398 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1614399 Getting block 4 of 7 Reserving size (2129466) 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 1291865 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1291866 Getting block 5 of 7 Reserving size (2129466) 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 2118718 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2118719 Getting block 6 of 7 Reserving size (2129466) 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 1698146 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1698147 Getting block 7 of 7 Reserving size (2129466) 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 1397835 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1397836 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2817853 fchr[G]: 5673174 fchr[T]: 8532156 fchr[$]: 11357150 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22768474 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEP_08586/tmp/segment_juncs.rev.1.ebwt Wrote 1419648 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEP_08586/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11357150 bwtLen: 11357151 sz: 2839288 bwtSz: 2839288 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 354911 offsSz: 1419644 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 25351 numSides: 50702 numLines: 50702 ebwtTotLen: 3244928 ebwtTotSz: 3244928 reverse: 0 Total time for backward call to driver() for mirror index: 00:00:05