Settings: Output files: "/scratch/8793100.1.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/8793100.1.linga/tophat2/tmp/segment_juncs.fa Reading reference sizes Time reading reference sizes: 00:00:01 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 2760037 Using parameters --bmax 2070028 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2070028 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 6; iterating... 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 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.22668e+06 (target: 2070027) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2070028) 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 950212 (Using difference cover) Sorting block time: 00:00:00 Returning block of 950213 Getting block 2 of 9 Reserving size (2070028) 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 1489119 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1489120 Getting block 3 of 9 Reserving size (2070028) 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 1037160 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1037161 Getting block 4 of 9 Reserving size (2070028) 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 1633090 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1633091 Getting block 5 of 9 Reserving size (2070028) 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 690047 (Using difference cover) Sorting block time: 00:00:00 Returning block of 690048 Getting block 6 of 9 Reserving size (2070028) 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 1551667 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1551668 Getting block 7 of 9 Reserving size (2070028) 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 1173082 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1173083 Getting block 8 of 9 Reserving size (2070028) 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 1296640 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1296641 Getting block 9 of 9 Reserving size (2070028) 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 1219125 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1219126 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2742165 fchr[G]: 5504984 fchr[T]: 8271909 fchr[$]: 11040150 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22767741 bytes to primary EBWT file: /scratch/8793100.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2760044 bytes to secondary EBWT file: /scratch/8793100.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11040150 bwtLen: 11040151 sz: 2760038 bwtSz: 2760038 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 690010 offsSz: 2760040 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 57501 numLines: 57501 ebwtTotLen: 3680064 ebwtTotSz: 3680064 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:13 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: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2760037 Using parameters --bmax 2070028 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2070028 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 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: 1.22668e+06 (target: 2070027) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2070028) 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 941763 (Using difference cover) Sorting block time: 00:00:00 Returning block of 941764 Getting block 2 of 9 Reserving size (2070028) 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 1944367 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1944368 Getting block 3 of 9 Reserving size (2070028) 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 1689129 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1689130 Getting block 4 of 9 Reserving size (2070028) 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 557349 (Using difference cover) Sorting block time: 00:00:00 Returning block of 557350 Getting block 5 of 9 Reserving size (2070028) 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 1517746 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1517747 Getting block 6 of 9 Reserving size (2070028) 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 1370789 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1370790 Getting block 7 of 9 Reserving size (2070028) 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 705245 (Using difference cover) Sorting block time: 00:00:00 Returning block of 705246 Getting block 8 of 9 Reserving size (2070028) 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 2008327 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2008328 Getting block 9 of 9 Reserving size (2070028) 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 305427 (Using difference cover) Sorting block time: 00:00:00 Returning block of 305428 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2742165 fchr[G]: 5504984 fchr[T]: 8271909 fchr[$]: 11040150 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22767741 bytes to primary EBWT file: /scratch/8793100.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2760044 bytes to secondary EBWT file: /scratch/8793100.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11040150 bwtLen: 11040151 sz: 2760038 bwtSz: 2760038 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 690010 offsSz: 2760040 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 57501 numLines: 57501 ebwtTotLen: 3680064 ebwtTotSz: 3680064 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10