Settings: Output files: "/projects/NBL/HS1197/311NGAAXX_6/tophat/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/HS1197/311NGAAXX_6/tophat/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:24 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:15 bmax according to bmaxDivN setting: 55353696 Using parameters --bmax 41515272 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 41515272 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:14 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: 00:00:17 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: 00:00:17 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: 00:00:18 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:18 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.16307e+07 (target: 41515271) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (41515272) 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 35912825 (Using difference cover) Sorting block time: 00:00:54 Returning block of 35912826 Getting block 2 of 7 Reserving size (41515272) 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 32437645 (Using difference cover) Sorting block time: 00:00:54 Returning block of 32437646 Getting block 3 of 7 Reserving size (41515272) 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 34785933 (Using difference cover) Sorting block time: 00:01:05 Returning block of 34785934 Getting block 4 of 7 Reserving size (41515272) 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 33568985 (Using difference cover) Sorting block time: 00:01:01 Returning block of 33568986 Getting block 5 of 7 Reserving size (41515272) 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 31386668 (Using difference cover) Sorting block time: 00:01:00 Returning block of 31386669 Getting block 6 of 7 Reserving size (41515272) 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 36274374 (Using difference cover) Sorting block time: 00:01:08 Returning block of 36274375 Getting block 7 of 7 Reserving size (41515272) 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 17048351 (Using difference cover) Sorting block time: 00:00:24 Returning block of 17048352 Exited Ebwt loop fchr[A]: 0 fchr[C]: 58586406 fchr[G]: 110802426 fchr[T]: 163196341 fchr[$]: 221414787 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 404655653 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_6/tophat/tmp/segment_juncs.1.ebwt Wrote 27676856 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_6/tophat/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 221414787 bwtLen: 221414788 sz: 55353697 bwtSz: 55353697 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6919213 offsSz: 27676852 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 494230 numSides: 988460 numLines: 988460 ebwtTotLen: 63261440 ebwtTotSz: 63261440 Total time for call to driver() for forward index: 00:10:56 Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:15 bmax according to bmaxDivN setting: 55353696 Using parameters --bmax 41515272 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 41515272 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:13 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: 00:00:19 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: 00:00:15 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.16307e+07 (target: 41515271) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (41515272) 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 36314379 (Using difference cover) Sorting block time: 00:00:55 Returning block of 36314380 Getting block 2 of 7 Reserving size (41515272) 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 10535201 (Using difference cover) Sorting block time: 00:00:19 Returning block of 10535202 Getting block 3 of 7 Reserving size (41515272) 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 39589990 (Using difference cover) Sorting block time: 00:01:13 Returning block of 39589991 Getting block 4 of 7 Reserving size (41515272) 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 39500938 (Using difference cover) Sorting block time: 00:01:16 Returning block of 39500939 Getting block 5 of 7 Reserving size (41515272) 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 18465732 (Using difference cover) Sorting block time: 00:00:38 Returning block of 18465733 Getting block 6 of 7 Reserving size (41515272) 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 38045128 (Using difference cover) Sorting block time: 00:01:08 Returning block of 38045129 Getting block 7 of 7 Reserving size (41515272) 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 38963413 (Using difference cover) Sorting block time: 00:01:04 Returning block of 38963414 Exited Ebwt loop fchr[A]: 0 fchr[C]: 58586406 fchr[G]: 110802426 fchr[T]: 163196341 fchr[$]: 221414787 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 404655653 bytes to primary EBWT file: /projects/NBL/HS1197/311NGAAXX_6/tophat/tmp/segment_juncs.rev.1.ebwt Wrote 27676856 bytes to secondary EBWT file: /projects/NBL/HS1197/311NGAAXX_6/tophat/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 221414787 bwtLen: 221414788 sz: 55353697 bwtSz: 55353697 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6919213 offsSz: 27676852 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 494230 numSides: 988460 numLines: 988460 ebwtTotLen: 63261440 ebwtTotSz: 63261440 Total time for backward call to driver() for mirror index: 00:10:34