Settings: Output files: "/scratch/8792790.1.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/8792790.1.linga/tophat2/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: 00:00:01 bmax according to bmaxDivN setting: 2515837 Using parameters --bmax 1886878 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1886878 --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 Avg bucket size: 1.25792e+06 (target: 1886877) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1886878) 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 725767 (Using difference cover) Sorting block time: 00:00:00 Returning block of 725768 Getting block 2 of 8 Reserving size (1886878) 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 1664257 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1664258 Getting block 3 of 8 Reserving size (1886878) 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 1846340 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1846341 Getting block 4 of 8 Reserving size (1886878) 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 270048 (Using difference cover) Sorting block time: 00:00:00 Returning block of 270049 Getting block 5 of 8 Reserving size (1886878) 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 1826338 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1826339 Getting block 6 of 8 Reserving size (1886878) 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 1381608 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1381609 Getting block 7 of 8 Reserving size (1886878) 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 1449984 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1449985 Getting block 8 of 8 Reserving size (1886878) 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 899001 (Using difference cover) Sorting block time: 00:00:00 Returning block of 899002 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2490991 fchr[G]: 5029443 fchr[T]: 7563144 fchr[$]: 10063350 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21130949 bytes to primary EBWT file: /scratch/8792790.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2515844 bytes to secondary EBWT file: /scratch/8792790.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10063350 bwtLen: 10063351 sz: 2515838 bwtSz: 2515838 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 628960 offsSz: 2515840 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52414 numLines: 52414 ebwtTotLen: 3354496 ebwtTotSz: 3354496 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:08 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: 2515837 Using parameters --bmax 1886878 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1886878 --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 2, 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: 1.43762e+06 (target: 1886877) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1886878) 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 1206899 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1206900 Getting block 2 of 7 Reserving size (1886878) 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 1535694 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1535695 Getting block 3 of 7 Reserving size (1886878) 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 1693046 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1693047 Getting block 4 of 7 Reserving size (1886878) 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 1318478 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1318479 Getting block 5 of 7 Reserving size (1886878) 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 916566 (Using difference cover) Sorting block time: 00:00:00 Returning block of 916567 Getting block 6 of 7 Reserving size (1886878) 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 1883158 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1883159 Getting block 7 of 7 Reserving size (1886878) 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 1509503 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1509504 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2490991 fchr[G]: 5029443 fchr[T]: 7563144 fchr[$]: 10063350 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21130949 bytes to primary EBWT file: /scratch/8792790.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2515844 bytes to secondary EBWT file: /scratch/8792790.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10063350 bwtLen: 10063351 sz: 2515838 bwtSz: 2515838 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 628960 offsSz: 2515840 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52414 numLines: 52414 ebwtTotLen: 3354496 ebwtTotSz: 3354496 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:09