Settings: Output files: "/scratch/8793237.1.linga/tophat2/tmp/segment_juncs.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) 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: /scratch/8793237.1.linga/tophat2/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: 2594100 Using parameters --bmax 1945575 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1945575 --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 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 Avg bucket size: 1.48234e+06 (target: 1945574) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1945575) 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 1127002 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1127003 Getting block 2 of 7 Reserving size (1945575) 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 1941124 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1941125 Getting block 3 of 7 Reserving size (1945575) 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 1135309 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1135310 Getting block 4 of 7 Reserving size (1945575) 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 1761694 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1761695 Getting block 5 of 7 Reserving size (1945575) 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 1288273 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1288274 Getting block 6 of 7 Reserving size (1945575) 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 1247137 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1247138 Getting block 7 of 7 Reserving size (1945575) 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 1875855 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1875856 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2577028 fchr[G]: 5181692 fchr[T]: 7785655 fchr[$]: 10376400 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21654623 bytes to primary EBWT file: /scratch/8793237.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2594108 bytes to secondary EBWT file: /scratch/8793237.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10376400 bwtLen: 10376401 sz: 2594100 bwtSz: 2594101 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 648526 offsSz: 2594104 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 54044 numLines: 54044 ebwtTotLen: 3458816 ebwtTotSz: 3458816 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:10 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2594100 Using parameters --bmax 1945575 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1945575 --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 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 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: 1.29705e+06 (target: 1945574) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1945575) 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 666860 (Using difference cover) Sorting block time: 00:00:00 Returning block of 666861 Getting block 2 of 8 Reserving size (1945575) 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 1664765 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1664766 Getting block 3 of 8 Reserving size (1945575) 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 1217250 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1217251 Getting block 4 of 8 Reserving size (1945575) 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 1164425 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1164426 Getting block 5 of 8 Reserving size (1945575) 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 1724797 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1724798 Getting block 6 of 8 Reserving size (1945575) 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 1665284 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1665285 Getting block 7 of 8 Reserving size (1945575) 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 1753346 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1753347 Getting block 8 of 8 Reserving size (1945575) 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 519666 (Using difference cover) Sorting block time: 00:00:00 Returning block of 519667 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2577028 fchr[G]: 5181692 fchr[T]: 7785655 fchr[$]: 10376400 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21654623 bytes to primary EBWT file: /scratch/8793237.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2594108 bytes to secondary EBWT file: /scratch/8793237.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10376400 bwtLen: 10376401 sz: 2594100 bwtSz: 2594101 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 648526 offsSz: 2594104 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 54044 numLines: 54044 ebwtTotLen: 3458816 ebwtTotSz: 3458816 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10