Settings: Output files: "/scratch/9142559.1.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/9142559.1.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: 6039390 Using parameters --bmax 4529543 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4529543 --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: 00:00:01 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 5; 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 Avg bucket size: 2.68417e+06 (target: 4529542) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (4529543) 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 2633501 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2633502 Getting block 2 of 9 Reserving size (4529543) 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 3499560 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3499561 Getting block 3 of 9 Reserving size (4529543) 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 1646758 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1646759 Getting block 4 of 9 Reserving size (4529543) 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 2924433 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2924434 Getting block 5 of 9 Reserving size (4529543) 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 1749940 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1749941 Getting block 6 of 9 Reserving size (4529543) 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 3953968 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3953969 Getting block 7 of 9 Reserving size (4529543) 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 2905234 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2905235 Getting block 8 of 9 Reserving size (4529543) 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 2673238 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2673239 Getting block 9 of 9 Reserving size (4529543) 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 2170921 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2170922 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5883733 fchr[G]: 12064599 fchr[T]: 18101127 fchr[$]: 24157561 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 44857020 bytes to primary EBWT file: /scratch/9142559.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 6039396 bytes to secondary EBWT file: /scratch/9142559.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 24157561 bwtLen: 24157562 sz: 6039391 bwtSz: 6039391 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1509848 offsSz: 6039392 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 125821 numLines: 125821 ebwtTotLen: 8052544 ebwtTotSz: 8052544 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:30 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: 00:00:01 bmax according to bmaxDivN setting: 6039390 Using parameters --bmax 4529543 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4529543 --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: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.45108e+06 (target: 4529542) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4529543) 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 4097041 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4097042 Getting block 2 of 7 Reserving size (4529543) 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 2856166 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2856167 Getting block 3 of 7 Reserving size (4529543) 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 2879317 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2879318 Getting block 4 of 7 Reserving size (4529543) 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 4035658 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4035659 Getting block 5 of 7 Reserving size (4529543) 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 4142652 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4142653 Getting block 6 of 7 Reserving size (4529543) 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 3588924 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3588925 Getting block 7 of 7 Reserving size (4529543) 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 2557797 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2557798 Exited Ebwt loop fchr[A]: 0 fchr[C]: 5883733 fchr[G]: 12064599 fchr[T]: 18101127 fchr[$]: 24157561 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 44857020 bytes to primary EBWT file: /scratch/9142559.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 6039396 bytes to secondary EBWT file: /scratch/9142559.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 24157561 bwtLen: 24157562 sz: 6039391 bwtSz: 6039391 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1509848 offsSz: 6039392 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 125821 numLines: 125821 ebwtTotLen: 8052544 ebwtTotSz: 8052544 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:29