Settings: Output files: "/scratch/9351453.1.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/9351453.1.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: 00:00:01 bmax according to bmaxDivN setting: 4204057 Using parameters --bmax 3153043 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3153043 --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 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: 2.40232e+06 (target: 3153042) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (3153043) 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 3018555 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3018556 Getting block 2 of 7 Reserving size (3153043) 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 2611721 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2611722 Getting block 3 of 7 Reserving size (3153043) 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 2029776 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2029777 Getting block 4 of 7 Reserving size (3153043) 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 2007460 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2007461 Getting block 5 of 7 Reserving size (3153043) 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 2977684 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2977685 Getting block 6 of 7 Reserving size (3153043) 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 1566615 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1566616 Getting block 7 of 7 Reserving size (3153043) 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 2604412 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2604413 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4162139 fchr[G]: 8401225 fchr[T]: 12607693 fchr[$]: 16816229 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 31553050 bytes to primary EBWT file: /scratch/9351453.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 4204064 bytes to secondary EBWT file: /scratch/9351453.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16816229 bwtLen: 16816230 sz: 4204058 bwtSz: 4204058 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1051015 offsSz: 4204060 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 87585 numLines: 87585 ebwtTotLen: 5605440 ebwtTotSz: 5605440 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:22 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: 4204057 Using parameters --bmax 3153043 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3153043 --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: 00:00:01 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 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 2, merged 2; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 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: 1.86847e+06 (target: 3153042) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (3153043) 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 795989 (Using difference cover) Sorting block time: 00:00:00 Returning block of 795990 Getting block 2 of 9 Reserving size (3153043) 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 2362533 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2362534 Getting block 3 of 9 Reserving size (3153043) 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 1674646 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1674647 Getting block 4 of 9 Reserving size (3153043) 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 1996485 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1996486 Getting block 5 of 9 Reserving size (3153043) 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 1544631 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1544632 Getting block 6 of 9 Reserving size (3153043) 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 2528299 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2528300 Getting block 7 of 9 Reserving size (3153043) 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 1677889 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1677890 Getting block 8 of 9 Reserving size (3153043) 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 1505796 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1505797 Getting block 9 of 9 Reserving size (3153043) 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 2729953 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2729954 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4162139 fchr[G]: 8401225 fchr[T]: 12607693 fchr[$]: 16816229 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 31553050 bytes to primary EBWT file: /scratch/9351453.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 4204064 bytes to secondary EBWT file: /scratch/9351453.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 16816229 bwtLen: 16816230 sz: 4204058 bwtSz: 4204058 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1051015 offsSz: 4204060 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 87585 numLines: 87585 ebwtTotLen: 5605440 ebwtTotSz: 5605440 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:23