Settings: Output files: "/scratch/8793325.1.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/8793325.1.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: 2544825 Using parameters --bmax 1908619 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1908619 --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 Avg bucket size: 1.45418e+06 (target: 1908618) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1908619) 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 1390715 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1390716 Getting block 2 of 7 Reserving size (1908619) 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 1905347 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1905348 Getting block 3 of 7 Reserving size (1908619) 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 1317074 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1317075 Getting block 4 of 7 Reserving size (1908619) 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 1482134 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1482135 Getting block 5 of 7 Reserving size (1908619) 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 1780990 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1780991 Getting block 6 of 7 Reserving size (1908619) 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 957265 (Using difference cover) Sorting block time: 00:00:00 Returning block of 957266 Getting block 7 of 7 Reserving size (1908619) 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 1345769 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1345770 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2526534 fchr[G]: 5083983 fchr[T]: 7641403 fchr[$]: 10179300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21324645 bytes to primary EBWT file: /scratch/8793325.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2544832 bytes to secondary EBWT file: /scratch/8793325.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10179300 bwtLen: 10179301 sz: 2544825 bwtSz: 2544826 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 636207 offsSz: 2544828 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 53018 numLines: 53018 ebwtTotLen: 3393152 ebwtTotSz: 3393152 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: 00:00:00 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 2544825 Using parameters --bmax 1908619 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1908619 --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 Split 1, merged 2; 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: 1.45418e+06 (target: 1908618) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1908619) 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 1408018 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1408019 Getting block 2 of 7 Reserving size (1908619) 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 1402824 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1402825 Getting block 3 of 7 Reserving size (1908619) 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 1430552 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1430553 Getting block 4 of 7 Reserving size (1908619) 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 1876772 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1876773 Getting block 5 of 7 Reserving size (1908619) 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 1179605 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1179606 Getting block 6 of 7 Reserving size (1908619) 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 1007025 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1007026 Getting block 7 of 7 Reserving size (1908619) 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 1874498 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1874499 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2526534 fchr[G]: 5083983 fchr[T]: 7641403 fchr[$]: 10179300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21324645 bytes to primary EBWT file: /scratch/8793325.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2544832 bytes to secondary EBWT file: /scratch/8793325.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10179300 bwtLen: 10179301 sz: 2544825 bwtSz: 2544826 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 636207 offsSz: 2544828 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 53018 numLines: 53018 ebwtTotLen: 3393152 ebwtTotSz: 3393152 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:12