Settings: Output files: "/scratch/8793134.1.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/8793134.1.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: 00:00:00 bmax according to bmaxDivN setting: 2669050 Using parameters --bmax 2001788 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2001788 --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 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.33452e+06 (target: 2001787) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2001788) 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 1310415 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1310416 Getting block 2 of 8 Reserving size (2001788) 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 1261213 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1261214 Getting block 3 of 8 Reserving size (2001788) 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 1577897 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1577898 Getting block 4 of 8 Reserving size (2001788) 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 1182340 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1182341 Getting block 5 of 8 Reserving size (2001788) 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 1320119 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1320120 Getting block 6 of 8 Reserving size (2001788) 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 898728 (Using difference cover) Sorting block time: 00:00:00 Returning block of 898729 Getting block 7 of 8 Reserving size (2001788) 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 1763258 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1763259 Getting block 8 of 8 Reserving size (2001788) 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 1362223 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1362224 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2650086 fchr[G]: 5331869 fchr[T]: 8008009 fchr[$]: 10676200 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22161187 bytes to primary EBWT file: /scratch/8793134.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2669056 bytes to secondary EBWT file: /scratch/8793134.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10676200 bwtLen: 10676201 sz: 2669050 bwtSz: 2669051 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 667263 offsSz: 2669052 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 55606 numLines: 55606 ebwtTotLen: 3558784 ebwtTotSz: 3558784 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:09 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 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2669050 Using parameters --bmax 2001788 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2001788 --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 1, merged 6; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:01 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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.33452e+06 (target: 2001787) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (2001788) 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 1632440 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1632441 Getting block 2 of 8 Reserving size (2001788) 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 1623770 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1623771 Getting block 3 of 8 Reserving size (2001788) 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 495382 (Using difference cover) Sorting block time: 00:00:00 Returning block of 495383 Getting block 4 of 8 Reserving size (2001788) 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 1564244 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1564245 Getting block 5 of 8 Reserving size (2001788) 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 1172676 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1172677 Getting block 6 of 8 Reserving size (2001788) 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 1399294 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1399295 Getting block 7 of 8 Reserving size (2001788) 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 1934143 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1934144 Getting block 8 of 8 Reserving size (2001788) 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 854244 (Using difference cover) Sorting block time: 00:00:00 Returning block of 854245 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2650086 fchr[G]: 5331869 fchr[T]: 8008009 fchr[$]: 10676200 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22161187 bytes to primary EBWT file: /scratch/8793134.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2669056 bytes to secondary EBWT file: /scratch/8793134.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10676200 bwtLen: 10676201 sz: 2669050 bwtSz: 2669051 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 667263 offsSz: 2669052 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 55606 numLines: 55606 ebwtTotLen: 3558784 ebwtTotSz: 3558784 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10