Settings: Output files: "/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW1_08587/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_PrEW1_08587/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: 2855237 Using parameters --bmax 2141428 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2141428 --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: 00:00:00 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: 1.42762e+06 (target: 2141427) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2141428) 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 1185913 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1185914 Getting block 2 of 8 Reserving size (2141428) 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 1299862 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1299863 Getting block 3 of 8 Reserving size (2141428) 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 2081137 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2081138 Getting block 4 of 8 Reserving size (2141428) 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 507937 (Using difference cover) Sorting block time: 00:00:00 Returning block of 507938 Getting block 5 of 8 Reserving size (2141428) 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 2137932 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2137933 Getting block 6 of 8 Reserving size (2141428) 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 1261347 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1261348 Getting block 7 of 8 Reserving size (2141428) 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 1222526 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1222527 Getting block 8 of 8 Reserving size (2141428) 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 1724289 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1724290 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2836385 fchr[G]: 5704476 fchr[T]: 8580332 fchr[$]: 11420950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22872627 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW1_08587/tmp/segment_juncs.1.ebwt Wrote 1427624 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW1_08587/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11420950 bwtLen: 11420951 sz: 2855238 bwtSz: 2855238 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 356905 offsSz: 1427620 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 25494 numSides: 50988 numLines: 50988 ebwtTotLen: 3263232 ebwtTotSz: 3263232 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: 2855237 Using parameters --bmax 2141428 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2141428 --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 2, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 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: 1.42762e+06 (target: 2141427) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2141428) 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 1197858 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1197859 Getting block 2 of 8 Reserving size (2141428) 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 1064661 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1064662 Getting block 3 of 8 Reserving size (2141428) 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 1923715 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1923716 Getting block 4 of 8 Reserving size (2141428) 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 1591813 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1591814 Getting block 5 of 8 Reserving size (2141428) 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 1605452 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1605453 Getting block 6 of 8 Reserving size (2141428) 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 1745112 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1745113 Getting block 7 of 8 Reserving size (2141428) 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 2016459 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2016460 Getting block 8 of 8 Reserving size (2141428) 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 275873 (Using difference cover) Sorting block time: 00:00:01 Returning block of 275874 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2836385 fchr[G]: 5704476 fchr[T]: 8580332 fchr[$]: 11420950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22872627 bytes to primary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW1_08587/tmp/segment_juncs.rev.1.ebwt Wrote 1427624 bytes to secondary EBWT file: /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW1_08587/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11420950 bwtLen: 11420951 sz: 2855238 bwtSz: 2855238 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 356905 offsSz: 1427620 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 25494 numSides: 50988 numLines: 50988 ebwtTotLen: 3263232 ebwtTotSz: 3263232 reverse: 0 Total time for backward call to driver() for mirror index: 00:00:07