Settings: Output files: "/projects/NBL/HS1196/302NNAAXX_6/tophat_wj/tmp/segment_juncs.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) 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: /projects/NBL/HS1196/302NNAAXX_6/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:55 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:18 bmax according to bmaxDivN setting: 58303892 Using parameters --bmax 43727919 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 43727919 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:15 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:02 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:06 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: 00:00:26 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: 00:00:22 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.91519e+07 (target: 43727918) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (43727919) 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: 00:00:07 Sorting block of length 25852602 (Using difference cover) Sorting block time: 00:00:37 Returning block of 25852603 Getting block 2 of 8 Reserving size (43727919) 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: 00:00:08 Sorting block of length 30451780 (Using difference cover) Sorting block time: 00:00:54 Returning block of 30451781 Getting block 3 of 8 Reserving size (43727919) 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: 00:00:10 Sorting block of length 32120303 (Using difference cover) Sorting block time: 00:00:57 Returning block of 32120304 Getting block 4 of 8 Reserving size (43727919) 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: 00:00:10 Sorting block of length 19144856 (Using difference cover) Sorting block time: 00:00:38 Returning block of 19144857 Getting block 5 of 8 Reserving size (43727919) 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: 00:00:11 Sorting block of length 24788283 (Using difference cover) Sorting block time: 00:00:43 Returning block of 24788284 Getting block 6 of 8 Reserving size (43727919) 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: 00:00:11 Sorting block of length 32577571 (Using difference cover) Sorting block time: 00:01:00 Returning block of 32577572 Getting block 7 of 8 Reserving size (43727919) 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: 00:00:12 Sorting block of length 26753051 (Using difference cover) Sorting block time: 00:00:47 Returning block of 26753052 Getting block 8 of 8 Reserving size (43727919) 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: 00:00:07 Sorting block of length 41527116 (Using difference cover) Sorting block time: 00:01:04 Returning block of 41527117 Exited Ebwt loop fchr[A]: 0 fchr[C]: 61679336 fchr[G]: 117114954 fchr[T]: 171776630 fchr[$]: 233215569 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 425727182 bytes to primary EBWT file: /projects/NBL/HS1196/302NNAAXX_6/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 29151952 bytes to secondary EBWT file: /projects/NBL/HS1196/302NNAAXX_6/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 233215569 bwtLen: 233215570 sz: 58303893 bwtSz: 58303893 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 7287987 offsSz: 29151948 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 520571 numSides: 1041142 numLines: 1041142 ebwtTotLen: 66633088 ebwtTotSz: 66633088 Total time for call to driver() for forward index: 00:11:46 Reading reference sizes Time reading reference sizes: 00:00:04 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:19 bmax according to bmaxDivN setting: 58303892 Using parameters --bmax 43727919 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 43727919 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:15 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:05 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: 00:00:26 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:22 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: 00:00:22 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.33165e+07 (target: 43727918) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (43727919) 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: 00:00:07 Sorting block of length 13704287 (Using difference cover) Sorting block time: 00:00:16 Returning block of 13704288 Getting block 2 of 7 Reserving size (43727919) 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: 00:00:08 Sorting block of length 36866750 (Using difference cover) Sorting block time: 00:01:03 Returning block of 36866751 Getting block 3 of 7 Reserving size (43727919) 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: 00:00:09 Sorting block of length 36262998 (Using difference cover) Sorting block time: 00:01:04 Returning block of 36262999 Getting block 4 of 7 Reserving size (43727919) 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: 00:00:10 Sorting block of length 22593982 (Using difference cover) Sorting block time: 00:00:41 Returning block of 22593983 Getting block 5 of 7 Reserving size (43727919) 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: 00:00:12 Sorting block of length 40774881 (Using difference cover) Sorting block time: 00:01:14 Returning block of 40774882 Getting block 6 of 7 Reserving size (43727919) 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: 00:00:12 Sorting block of length 39779355 (Using difference cover) Sorting block time: 00:01:07 Returning block of 39779356 Getting block 7 of 7 Reserving size (43727919) 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: 00:00:07 Sorting block of length 43233310 (Using difference cover) Sorting block time: 00:01:06 Returning block of 43233311 Exited Ebwt loop fchr[A]: 0 fchr[C]: 61679336 fchr[G]: 117114954 fchr[T]: 171776630 fchr[$]: 233215569 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 425727182 bytes to primary EBWT file: /projects/NBL/HS1196/302NNAAXX_6/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 29151952 bytes to secondary EBWT file: /projects/NBL/HS1196/302NNAAXX_6/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 233215569 bwtLen: 233215570 sz: 58303893 bwtSz: 58303893 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 7287987 offsSz: 29151948 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 520571 numSides: 1041142 numLines: 1041142 ebwtTotLen: 66633088 ebwtTotSz: 66633088 Total time for backward call to driver() for mirror index: 00:10:58