Settings: Output files: "/scratch/8793280.1.c/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/8793280.1.c/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: 00:00:00 bmax according to bmaxDivN setting: 2711900 Using parameters --bmax 2033925 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2033925 --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 2, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.54966e+06 (target: 2033924) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2033925) 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 1693623 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1693624 Getting block 2 of 7 Reserving size (2033925) 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 1418758 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1418759 Getting block 3 of 7 Reserving size (2033925) 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 1973278 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1973279 Getting block 4 of 7 Reserving size (2033925) 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 1502573 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1502574 Getting block 5 of 7 Reserving size (2033925) 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 1872500 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1872501 Getting block 6 of 7 Reserving size (2033925) 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 1374050 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1374051 Getting block 7 of 7 Reserving size (2033925) 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 1012812 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1012813 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2697946 fchr[G]: 5415622 fchr[T]: 8122320 fchr[$]: 10847600 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22444888 bytes to primary EBWT file: /scratch/8793280.1.c/tophat2/tmp/segment_juncs.1.bt2 Wrote 2711908 bytes to secondary EBWT file: /scratch/8793280.1.c/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10847600 bwtLen: 10847601 sz: 2711900 bwtSz: 2711901 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 677976 offsSz: 2711904 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 56498 numLines: 56498 ebwtTotLen: 3615872 ebwtTotSz: 3615872 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:05 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: 2711900 Using parameters --bmax 2033925 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2033925 --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 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.35595e+06 (target: 2033924) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2033925) 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 1535108 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1535109 Getting block 2 of 8 Reserving size (2033925) 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 1823955 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1823956 Getting block 3 of 8 Reserving size (2033925) 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 1576151 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1576152 Getting block 4 of 8 Reserving size (2033925) 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 1248054 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1248055 Getting block 5 of 8 Reserving size (2033925) 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 1994820 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1994821 Getting block 6 of 8 Reserving size (2033925) 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 391088 (Using difference cover) Sorting block time: 00:00:00 Returning block of 391089 Getting block 7 of 8 Reserving size (2033925) 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 1845542 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1845543 Getting block 8 of 8 Reserving size (2033925) 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 432875 (Using difference cover) Sorting block time: 00:00:00 Returning block of 432876 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2697946 fchr[G]: 5415622 fchr[T]: 8122320 fchr[$]: 10847600 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22444888 bytes to primary EBWT file: /scratch/8793280.1.c/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2711908 bytes to secondary EBWT file: /scratch/8793280.1.c/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10847600 bwtLen: 10847601 sz: 2711900 bwtSz: 2711901 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 677976 offsSz: 2711904 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 56498 numLines: 56498 ebwtTotLen: 3615872 ebwtTotSz: 3615872 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:05