Settings: Output files: "/projects/NBL/HS1196/3153YAAXX_8/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/HS1196/3153YAAXX_8/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:10 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:09 bmax according to bmaxDivN setting: 39018735 Using parameters --bmax 29264052 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 29264052 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:07 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: 00:00:03 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: 00:00:13 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.60125e+07 (target: 29264051) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (29264052) 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: 00:00:03 Sorting block of length 27881277 (Using difference cover) Sorting block time: 00:00:33 Returning block of 27881278 Getting block 2 of 6 Reserving size (29264052) 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: 00:00:04 Sorting block of length 27791670 (Using difference cover) Sorting block time: 00:00:36 Returning block of 27791671 Getting block 3 of 6 Reserving size (29264052) 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: 00:00:05 Sorting block of length 23484807 (Using difference cover) Sorting block time: 00:00:30 Returning block of 23484808 Getting block 4 of 6 Reserving size (29264052) 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: 00:00:06 Sorting block of length 25855806 (Using difference cover) Sorting block time: 00:00:33 Returning block of 25855807 Getting block 5 of 6 Reserving size (29264052) 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: 00:00:06 Sorting block of length 23380770 (Using difference cover) Sorting block time: 00:00:29 Returning block of 23380771 Getting block 6 of 6 Reserving size (29264052) 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: 00:00:03 Sorting block of length 27680607 (Using difference cover) Sorting block time: 00:00:31 Returning block of 27680608 Exited Ebwt loop fchr[A]: 0 fchr[C]: 39837626 fchr[G]: 78484346 fchr[T]: 116230986 fchr[$]: 156074942 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 286309388 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_8/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 19509372 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_8/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 156074942 bwtLen: 156074943 sz: 39018736 bwtSz: 39018736 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4877342 offsSz: 19509368 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 348382 numSides: 696764 numLines: 696764 ebwtTotLen: 44592896 ebwtTotSz: 44592896 Total time for call to driver() for forward index: 00:04:47 Reading reference sizes Time reading reference sizes: 00:00:03 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:09 bmax according to bmaxDivN setting: 39018735 Using parameters --bmax 29264052 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 29264052 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:07 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: 00:00:02 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: 00:00:13 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: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.95094e+07 (target: 29264051) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (29264052) 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: 00:00:02 Sorting block of length 7878740 (Using difference cover) Sorting block time: 00:00:08 Returning block of 7878741 Getting block 2 of 8 Reserving size (29264052) 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: 00:00:04 Sorting block of length 27706628 (Using difference cover) Sorting block time: 00:00:34 Returning block of 27706629 Getting block 3 of 8 Reserving size (29264052) 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: 00:00:04 Sorting block of length 14443214 (Using difference cover) Sorting block time: 00:00:18 Returning block of 14443215 Getting block 4 of 8 Reserving size (29264052) 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: 00:00:05 Sorting block of length 19637256 (Using difference cover) Sorting block time: 00:00:26 Returning block of 19637257 Getting block 5 of 8 Reserving size (29264052) 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: 00:00:05 Sorting block of length 28789742 (Using difference cover) Sorting block time: 00:00:36 Returning block of 28789743 Getting block 6 of 8 Reserving size (29264052) 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: 00:00:05 Sorting block of length 16586131 (Using difference cover) Sorting block time: 00:00:20 Returning block of 16586132 Getting block 7 of 8 Reserving size (29264052) 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: 00:00:06 Sorting block of length 29043300 (Using difference cover) Sorting block time: 00:00:35 Returning block of 29043301 Getting block 8 of 8 Reserving size (29264052) 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: 00:00:04 Sorting block of length 11989924 (Using difference cover) Sorting block time: 00:00:11 Returning block of 11989925 Exited Ebwt loop fchr[A]: 0 fchr[C]: 39837626 fchr[G]: 78484346 fchr[T]: 116230986 fchr[$]: 156074942 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 286309388 bytes to primary EBWT file: /projects/NBL/HS1196/3153YAAXX_8/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 19509372 bytes to secondary EBWT file: /projects/NBL/HS1196/3153YAAXX_8/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 156074942 bwtLen: 156074943 sz: 39018736 bwtSz: 39018736 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4877342 offsSz: 19509368 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 348382 numSides: 696764 numLines: 696764 ebwtTotLen: 44592896 ebwtTotSz: 44592896 Total time for backward call to driver() for mirror index: 00:04:58