Settings: Output files: "/scratch/9328370.1.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/9328370.1.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: 4478413 Using parameters --bmax 3358810 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3358810 --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 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.23921e+06 (target: 3358809) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3358810) 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 2315311 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2315312 Getting block 2 of 8 Reserving size (3358810) 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 2755599 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2755600 Getting block 3 of 8 Reserving size (3358810) 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 1138346 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1138347 Getting block 4 of 8 Reserving size (3358810) 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 2860135 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2860136 Getting block 5 of 8 Reserving size (3358810) 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 1924315 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1924316 Getting block 6 of 8 Reserving size (3358810) 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 3072814 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3072815 Getting block 7 of 8 Reserving size (3358810) 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 538721 (Using difference cover) Sorting block time: 00:00:01 Returning block of 538722 Getting block 8 of 8 Reserving size (3358810) 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 3308405 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3308406 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4438332 fchr[G]: 8998086 fchr[T]: 13434624 fchr[$]: 17913653 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33319390 bytes to primary EBWT file: /scratch/9328370.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 4478420 bytes to secondary EBWT file: /scratch/9328370.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17913653 bwtLen: 17913654 sz: 4478414 bwtSz: 4478414 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1119604 offsSz: 4478416 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 93301 numLines: 93301 ebwtTotLen: 5971264 ebwtTotSz: 5971264 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:21 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4478413 Using parameters --bmax 3358810 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3358810 --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 3, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 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: 1.9904e+06 (target: 3358809) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (3358810) 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 3247029 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3247030 Getting block 2 of 9 Reserving size (3358810) 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 1571771 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1571772 Getting block 3 of 9 Reserving size (3358810) 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 2315321 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2315322 Getting block 4 of 9 Reserving size (3358810) 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 1703163 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1703164 Getting block 5 of 9 Reserving size (3358810) 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 1941722 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1941723 Getting block 6 of 9 Reserving size (3358810) 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 3217444 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3217445 Getting block 7 of 9 Reserving size (3358810) 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 151101 (Using difference cover) Sorting block time: 00:00:00 Returning block of 151102 Getting block 8 of 9 Reserving size (3358810) 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 3240141 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3240142 Getting block 9 of 9 Reserving size (3358810) 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 525953 (Using difference cover) Sorting block time: 00:00:01 Returning block of 525954 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4438332 fchr[G]: 8998086 fchr[T]: 13434624 fchr[$]: 17913653 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 33319390 bytes to primary EBWT file: /scratch/9328370.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 4478420 bytes to secondary EBWT file: /scratch/9328370.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 17913653 bwtLen: 17913654 sz: 4478414 bwtSz: 4478414 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1119604 offsSz: 4478416 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 93301 numLines: 93301 ebwtTotLen: 5971264 ebwtTotSz: 5971264 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:21