Settings: Output files: "/scratch/8792921.1.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/8792921.1.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: 00:00:00 bmax according to bmaxDivN setting: 2527762 Using parameters --bmax 1895822 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1895822 --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 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: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.26388e+06 (target: 1895821) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1895822) 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 1207275 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1207276 Getting block 2 of 8 Reserving size (1895822) 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 979451 (Using difference cover) Sorting block time: 00:00:00 Returning block of 979452 Getting block 3 of 8 Reserving size (1895822) 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 1190184 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1190185 Getting block 4 of 8 Reserving size (1895822) 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 1752351 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1752352 Getting block 5 of 8 Reserving size (1895822) 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 1464604 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1464605 Getting block 6 of 8 Reserving size (1895822) 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 1113222 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1113223 Getting block 7 of 8 Reserving size (1895822) 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 1000736 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1000737 Getting block 8 of 8 Reserving size (1895822) 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 1403220 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1403221 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2513741 fchr[G]: 5064096 fchr[T]: 7606534 fchr[$]: 10111050 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21213296 bytes to primary EBWT file: /scratch/8792921.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2527768 bytes to secondary EBWT file: /scratch/8792921.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10111050 bwtLen: 10111051 sz: 2527763 bwtSz: 2527763 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 631941 offsSz: 2527764 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52662 numLines: 52662 ebwtTotLen: 3370368 ebwtTotSz: 3370368 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:08 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: 2527762 Using parameters --bmax 1895822 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1895822 --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 Avg bucket size: 1.44443e+06 (target: 1895821) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1895822) 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 1367932 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1367933 Getting block 2 of 7 Reserving size (1895822) 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 1172686 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1172687 Getting block 3 of 7 Reserving size (1895822) 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 832517 (Using difference cover) Sorting block time: 00:00:00 Returning block of 832518 Getting block 4 of 7 Reserving size (1895822) 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 1732893 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1732894 Getting block 5 of 7 Reserving size (1895822) 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 1630287 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1630288 Getting block 6 of 7 Reserving size (1895822) 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 1808680 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1808681 Getting block 7 of 7 Reserving size (1895822) 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 1566049 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1566050 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2513741 fchr[G]: 5064096 fchr[T]: 7606534 fchr[$]: 10111050 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21213296 bytes to primary EBWT file: /scratch/8792921.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2527768 bytes to secondary EBWT file: /scratch/8792921.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10111050 bwtLen: 10111051 sz: 2527763 bwtSz: 2527763 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 631941 offsSz: 2527764 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52662 numLines: 52662 ebwtTotLen: 3370368 ebwtTotSz: 3370368 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:07