Settings: Output files: "/scratch/8792762.1.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/8792762.1.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: 2521075 Using parameters --bmax 1890807 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1890807 --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 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 0; 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: 1.26054e+06 (target: 1890806) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1890807) 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 748926 (Using difference cover) Sorting block time: 00:00:00 Returning block of 748927 Getting block 2 of 8 Reserving size (1890807) 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 1486817 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1486818 Getting block 3 of 8 Reserving size (1890807) 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 954297 (Using difference cover) Sorting block time: 00:00:00 Returning block of 954298 Getting block 4 of 8 Reserving size (1890807) 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 1874345 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1874346 Getting block 5 of 8 Reserving size (1890807) 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 1343212 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1343213 Getting block 6 of 8 Reserving size (1890807) 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 1483481 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1483482 Getting block 7 of 8 Reserving size (1890807) 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 471575 (Using difference cover) Sorting block time: 00:00:00 Returning block of 471576 Getting block 8 of 8 Reserving size (1890807) 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 1721640 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1721641 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2502413 fchr[G]: 5041998 fchr[T]: 7586268 fchr[$]: 10084300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21170760 bytes to primary EBWT file: /scratch/8792762.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2521080 bytes to secondary EBWT file: /scratch/8792762.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10084300 bwtLen: 10084301 sz: 2521075 bwtSz: 2521076 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630269 offsSz: 2521076 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52523 numLines: 52523 ebwtTotLen: 3361472 ebwtTotSz: 3361472 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:09 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: 00:00:00 bmax according to bmaxDivN setting: 2521075 Using parameters --bmax 1890807 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1890807 --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 Avg bucket size: 1.44061e+06 (target: 1890806) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1890807) 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 1254384 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1254385 Getting block 2 of 7 Reserving size (1890807) 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 1454781 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1454782 Getting block 3 of 7 Reserving size (1890807) 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 471266 (Using difference cover) Sorting block time: 00:00:00 Returning block of 471267 Getting block 4 of 7 Reserving size (1890807) 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 1887093 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1887094 Getting block 5 of 7 Reserving size (1890807) 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 1521374 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1521375 Getting block 6 of 7 Reserving size (1890807) 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 1608942 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1608943 Getting block 7 of 7 Reserving size (1890807) 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 1886454 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1886455 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2502413 fchr[G]: 5041998 fchr[T]: 7586268 fchr[$]: 10084300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21170760 bytes to primary EBWT file: /scratch/8792762.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2521080 bytes to secondary EBWT file: /scratch/8792762.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10084300 bwtLen: 10084301 sz: 2521075 bwtSz: 2521076 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630269 offsSz: 2521076 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52523 numLines: 52523 ebwtTotLen: 3361472 ebwtTotSz: 3361472 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:06