Settings: Output files: "/scratch/9328368.1.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/9328368.1.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: 4925988 Using parameters --bmax 3694491 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3694491 --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 Avg bucket size: 2.46299e+06 (target: 3694490) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3694491) 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 2577613 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2577614 Getting block 2 of 8 Reserving size (3694491) 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 1762026 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1762027 Getting block 3 of 8 Reserving size (3694491) 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 3323142 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3323143 Getting block 4 of 8 Reserving size (3694491) 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 2788489 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2788490 Getting block 5 of 8 Reserving size (3694491) 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 3289438 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3289439 Getting block 6 of 8 Reserving size (3694491) 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 1149096 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1149097 Getting block 7 of 8 Reserving size (3694491) 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 3388645 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3388646 Getting block 8 of 8 Reserving size (3694491) 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 1425499 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1425500 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4879678 fchr[G]: 9897076 fchr[T]: 14762985 fchr[$]: 19703955 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 36229955 bytes to primary EBWT file: /scratch/9328368.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 4925996 bytes to secondary EBWT file: /scratch/9328368.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19703955 bwtLen: 19703956 sz: 4925989 bwtSz: 4925989 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1231498 offsSz: 4925992 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 102625 numLines: 102625 ebwtTotLen: 6568000 ebwtTotSz: 6568000 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:22 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 4925988 Using parameters --bmax 3694491 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3694491 --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 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:02 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.46299e+06 (target: 3694490) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3694491) 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 3288278 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3288279 Getting block 2 of 8 Reserving size (3694491) 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 1323652 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1323653 Getting block 3 of 8 Reserving size (3694491) 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 2521217 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2521218 Getting block 4 of 8 Reserving size (3694491) 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 2988768 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2988769 Getting block 5 of 8 Reserving size (3694491) 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 2866662 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2866663 Getting block 6 of 8 Reserving size (3694491) 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 1795568 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1795569 Getting block 7 of 8 Reserving size (3694491) 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 2799525 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2799526 Getting block 8 of 8 Reserving size (3694491) 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 2120278 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2120279 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4879678 fchr[G]: 9897076 fchr[T]: 14762985 fchr[$]: 19703955 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 36229955 bytes to primary EBWT file: /scratch/9328368.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 4925996 bytes to secondary EBWT file: /scratch/9328368.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 19703955 bwtLen: 19703956 sz: 4925989 bwtSz: 4925989 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1231498 offsSz: 4925992 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 102625 numLines: 102625 ebwtTotLen: 6568000 ebwtTotSz: 6568000 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:23