Settings: Output files: "/scratch/8793109.1.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/8793109.1.linga/tophat2/tmp/segment_juncs.fa 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: 00:00:01 bmax according to bmaxDivN setting: 2802112 Using parameters --bmax 2101584 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2101584 --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: 00:00:01 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 1, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.60121e+06 (target: 2101583) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2101584) 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 1646181 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1646182 Getting block 2 of 7 Reserving size (2101584) 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 1155172 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1155173 Getting block 3 of 7 Reserving size (2101584) 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 1655711 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1655712 Getting block 4 of 7 Reserving size (2101584) 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 1227530 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1227531 Getting block 5 of 7 Reserving size (2101584) 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 1949937 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1949938 Getting block 6 of 7 Reserving size (2101584) 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 1680501 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1680502 Getting block 7 of 7 Reserving size (2101584) 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 1893412 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1893413 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2795771 fchr[G]: 5601969 fchr[T]: 8403543 fchr[$]: 11208450 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23054919 bytes to primary EBWT file: /scratch/8793109.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2802120 bytes to secondary EBWT file: /scratch/8793109.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11208450 bwtLen: 11208451 sz: 2802113 bwtSz: 2802113 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 700529 offsSz: 2802116 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58378 numLines: 58378 ebwtTotLen: 3736192 ebwtTotSz: 3736192 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:11 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: 2802112 Using parameters --bmax 2101584 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2101584 --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 Split 3, merged 7; 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 Avg bucket size: 1.24538e+06 (target: 2101583) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2101584) 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 380388 (Using difference cover) Sorting block time: 00:00:00 Returning block of 380389 Getting block 2 of 9 Reserving size (2101584) 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 1773401 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1773402 Getting block 3 of 9 Reserving size (2101584) 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 619198 (Using difference cover) Sorting block time: 00:00:00 Returning block of 619199 Getting block 4 of 9 Reserving size (2101584) 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 1486780 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1486781 Getting block 5 of 9 Reserving size (2101584) 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 1952248 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1952249 Getting block 6 of 9 Reserving size (2101584) 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 1070209 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1070210 Getting block 7 of 9 Reserving size (2101584) 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 1046213 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1046214 Getting block 8 of 9 Reserving size (2101584) 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 1309232 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1309233 Getting block 9 of 9 Reserving size (2101584) 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 1570773 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1570774 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2795771 fchr[G]: 5601969 fchr[T]: 8403543 fchr[$]: 11208450 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23054919 bytes to primary EBWT file: /scratch/8793109.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2802120 bytes to secondary EBWT file: /scratch/8793109.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11208450 bwtLen: 11208451 sz: 2802113 bwtSz: 2802113 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 700529 offsSz: 2802116 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58378 numLines: 58378 ebwtTotLen: 3736192 ebwtTotSz: 3736192 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10