Settings: Output files: "/scratch/8793389.1.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/8793389.1.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: 2522050 Using parameters --bmax 1891538 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1891538 --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: 1.44117e+06 (target: 1891537) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1891538) 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 1171529 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1171530 Getting block 2 of 7 Reserving size (1891538) 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 1734554 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1734555 Getting block 3 of 7 Reserving size (1891538) 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 1546654 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1546655 Getting block 4 of 7 Reserving size (1891538) 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 1361052 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1361053 Getting block 5 of 7 Reserving size (1891538) 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 1881832 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1881833 Getting block 6 of 7 Reserving size (1891538) 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 1748684 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1748685 Getting block 7 of 7 Reserving size (1891538) 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 643889 (Using difference cover) Sorting block time: 00:00:00 Returning block of 643890 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2499009 fchr[G]: 5039708 fchr[T]: 7579619 fchr[$]: 10088200 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21172729 bytes to primary EBWT file: /scratch/8793389.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2522056 bytes to secondary EBWT file: /scratch/8793389.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10088200 bwtLen: 10088201 sz: 2522050 bwtSz: 2522051 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630513 offsSz: 2522052 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52543 numLines: 52543 ebwtTotLen: 3362752 ebwtTotSz: 3362752 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:07 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: 2522050 Using parameters --bmax 1891538 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1891538 --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: 00:00:00 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 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: 1.26102e+06 (target: 1891537) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1891538) 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 1346666 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1346667 Getting block 2 of 8 Reserving size (1891538) 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 671225 (Using difference cover) Sorting block time: 00:00:00 Returning block of 671226 Getting block 3 of 8 Reserving size (1891538) 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 1331596 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1331597 Getting block 4 of 8 Reserving size (1891538) 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 639185 (Using difference cover) Sorting block time: 00:00:00 Returning block of 639186 Getting block 5 of 8 Reserving size (1891538) 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 1424984 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1424985 Getting block 6 of 8 Reserving size (1891538) 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 1826017 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1826018 Getting block 7 of 8 Reserving size (1891538) 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 1010043 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1010044 Getting block 8 of 8 Reserving size (1891538) 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 1838477 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1838478 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2499009 fchr[G]: 5039708 fchr[T]: 7579619 fchr[$]: 10088200 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21172729 bytes to primary EBWT file: /scratch/8793389.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2522056 bytes to secondary EBWT file: /scratch/8793389.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10088200 bwtLen: 10088201 sz: 2522050 bwtSz: 2522051 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 630513 offsSz: 2522052 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52543 numLines: 52543 ebwtTotLen: 3362752 ebwtTotSz: 3362752 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:08