Settings: Output files: "/projects/NBL/HS1198/30UBRAAXX_4/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/HS1198/30UBRAAXX_4/tophat_wj/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:19 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:11 bmax according to bmaxDivN setting: 45114863 Using parameters --bmax 33836148 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 33836148 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:08 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: 00:00:15 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: 00:00:10 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: 00:00:11 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: 00:00:12 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.25574e+07 (target: 33836147) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (33836148) 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 19771156 (Using difference cover) Sorting block time: 00:00:18 Returning block of 19771157 Getting block 2 of 8 Reserving size (33836148) 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 31164316 (Using difference cover) Sorting block time: 00:00:35 Returning block of 31164317 Getting block 3 of 8 Reserving size (33836148) 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 24747066 (Using difference cover) Sorting block time: 00:00:33 Returning block of 24747067 Getting block 4 of 8 Reserving size (33836148) 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 20857937 (Using difference cover) Sorting block time: 00:00:25 Returning block of 20857938 Getting block 5 of 8 Reserving size (33836148) 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 13982754 (Using difference cover) Sorting block time: 00:00:17 Returning block of 13982755 Getting block 6 of 8 Reserving size (33836148) 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 24060162 (Using difference cover) Sorting block time: 00:00:27 Returning block of 24060163 Getting block 7 of 8 Reserving size (33836148) 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 20378415 (Using difference cover) Sorting block time: 00:00:25 Returning block of 20378416 Getting block 8 of 8 Reserving size (33836148) 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 25497641 (Using difference cover) Sorting block time: 00:00:26 Returning block of 25497642 Exited Ebwt loop fchr[A]: 0 fchr[C]: 48831070 fchr[G]: 91004082 fchr[T]: 131809328 fchr[$]: 180459454 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 330452037 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_4/tophat_wj/tmp/segment_juncs.1.ebwt Wrote 22557436 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_4/tophat_wj/tmp/segment_juncs.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 180459454 bwtLen: 180459455 sz: 45114864 bwtSz: 45114864 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5639358 offsSz: 22557432 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 402812 numSides: 805624 numLines: 805624 ebwtTotLen: 51559936 ebwtTotSz: 51559936 Total time for call to driver() for forward index: 00:06:06 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: 00:00:10 bmax according to bmaxDivN setting: 45114863 Using parameters --bmax 33836148 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 33836148 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:08 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: 00:00:15 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: 00:00:11 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 3.00766e+07 (target: 33836147) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 6 Reserving size (33836148) 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 24025704 (Using difference cover) Sorting block time: 00:00:24 Returning block of 24025705 Getting block 2 of 6 Reserving size (33836148) 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 30924904 (Using difference cover) Sorting block time: 00:00:35 Returning block of 30924905 Getting block 3 of 6 Reserving size (33836148) 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 29023934 (Using difference cover) Sorting block time: 00:00:36 Returning block of 29023935 Getting block 4 of 6 Reserving size (33836148) 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 31465235 (Using difference cover) Sorting block time: 00:00:40 Returning block of 31465236 Getting block 5 of 6 Reserving size (33836148) 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 32230946 (Using difference cover) Sorting block time: 00:00:36 Returning block of 32230947 Getting block 6 of 6 Reserving size (33836148) 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 32788726 (Using difference cover) Sorting block time: 00:00:35 Returning block of 32788727 Exited Ebwt loop fchr[A]: 0 fchr[C]: 48831070 fchr[G]: 91004082 fchr[T]: 131809328 fchr[$]: 180459454 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 330452037 bytes to primary EBWT file: /projects/NBL/HS1198/30UBRAAXX_4/tophat_wj/tmp/segment_juncs.rev.1.ebwt Wrote 22557436 bytes to secondary EBWT file: /projects/NBL/HS1198/30UBRAAXX_4/tophat_wj/tmp/segment_juncs.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 180459454 bwtLen: 180459455 sz: 45114864 bwtSz: 45114864 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 5639358 offsSz: 22557432 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 402812 numSides: 805624 numLines: 805624 ebwtTotLen: 51559936 ebwtTotSz: 51559936 Total time for backward call to driver() for mirror index: 00:05:19