Settings: Output files: "/scratch/8792998.1.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/8792998.1.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: 2685237 Using parameters --bmax 2013928 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2013928 --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: 00:00:01 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 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.53442e+06 (target: 2013927) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2013928) 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 1876661 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1876662 Getting block 2 of 7 Reserving size (2013928) 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 1863026 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1863027 Getting block 3 of 7 Reserving size (2013928) 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 1649883 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1649884 Getting block 4 of 7 Reserving size (2013928) 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 1617744 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1617745 Getting block 5 of 7 Reserving size (2013928) 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 819199 (Using difference cover) Sorting block time: 00:00:00 Returning block of 819200 Getting block 6 of 7 Reserving size (2013928) 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 1489371 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1489372 Getting block 7 of 7 Reserving size (2013928) 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 1425060 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1425061 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2665433 fchr[G]: 5360490 fchr[T]: 8054865 fchr[$]: 10740950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22266504 bytes to primary EBWT file: /scratch/8792998.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2685244 bytes to secondary EBWT file: /scratch/8792998.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10740950 bwtLen: 10740951 sz: 2685238 bwtSz: 2685238 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 671310 offsSz: 2685240 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 55943 numLines: 55943 ebwtTotLen: 3580352 ebwtTotSz: 3580352 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:11 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: 2685237 Using parameters --bmax 2013928 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2013928 --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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.34262e+06 (target: 2013927) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2013928) 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 550451 (Using difference cover) Sorting block time: 00:00:00 Returning block of 550452 Getting block 2 of 8 Reserving size (2013928) 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 1744260 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1744261 Getting block 3 of 8 Reserving size (2013928) 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 1384508 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1384509 Getting block 4 of 8 Reserving size (2013928) 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 1686220 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1686221 Getting block 5 of 8 Reserving size (2013928) 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 1627126 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1627127 Getting block 6 of 8 Reserving size (2013928) 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 807473 (Using difference cover) Sorting block time: 00:00:00 Returning block of 807474 Getting block 7 of 8 Reserving size (2013928) 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 1460099 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1460100 Getting block 8 of 8 Reserving size (2013928) 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 1480806 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1480807 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2665433 fchr[G]: 5360490 fchr[T]: 8054865 fchr[$]: 10740950 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22266504 bytes to primary EBWT file: /scratch/8792998.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2685244 bytes to secondary EBWT file: /scratch/8792998.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10740950 bwtLen: 10740951 sz: 2685238 bwtSz: 2685238 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 671310 offsSz: 2685240 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 55943 numLines: 55943 ebwtTotLen: 3580352 ebwtTotSz: 3580352 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10