Settings: Output files: "/scratch/8792861.1.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/8792861.1.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: 2533212 Using parameters --bmax 1899909 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1899909 --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 5; 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 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 Avg bucket size: 1.26661e+06 (target: 1899908) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (1899909) 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 839390 (Using difference cover) Sorting block time: 00:00:00 Returning block of 839391 Getting block 2 of 8 Reserving size (1899909) 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 1625888 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1625889 Getting block 3 of 8 Reserving size (1899909) 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 1040976 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1040977 Getting block 4 of 8 Reserving size (1899909) 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 1882342 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1882343 Getting block 5 of 8 Reserving size (1899909) 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 746132 (Using difference cover) Sorting block time: 00:00:00 Returning block of 746133 Getting block 6 of 8 Reserving size (1899909) 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 1755284 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1755285 Getting block 7 of 8 Reserving size (1899909) 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 1867576 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1867577 Getting block 8 of 8 Reserving size (1899909) 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 375255 (Using difference cover) Sorting block time: 00:00:00 Returning block of 375256 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2516691 fchr[G]: 5062185 fchr[T]: 7614650 fchr[$]: 10132850 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21248189 bytes to primary EBWT file: /scratch/8792861.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2533220 bytes to secondary EBWT file: /scratch/8792861.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10132850 bwtLen: 10132851 sz: 2533213 bwtSz: 2533213 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 633304 offsSz: 2533216 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52776 numLines: 52776 ebwtTotLen: 3377664 ebwtTotSz: 3377664 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: 00:00:01 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2533212 Using parameters --bmax 1899909 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1899909 --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 5; 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: 1.44755e+06 (target: 1899908) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (1899909) 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 1553052 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1553053 Getting block 2 of 7 Reserving size (1899909) 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 1812360 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1812361 Getting block 3 of 7 Reserving size (1899909) 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 1131302 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1131303 Getting block 4 of 7 Reserving size (1899909) 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 1127277 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1127278 Getting block 5 of 7 Reserving size (1899909) 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 1512135 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1512136 Getting block 6 of 7 Reserving size (1899909) 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 1132274 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1132275 Getting block 7 of 7 Reserving size (1899909) 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 1864444 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1864445 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2516691 fchr[G]: 5062185 fchr[T]: 7614650 fchr[$]: 10132850 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 21248189 bytes to primary EBWT file: /scratch/8792861.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2533220 bytes to secondary EBWT file: /scratch/8792861.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 10132850 bwtLen: 10132851 sz: 2533213 bwtSz: 2533213 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 633304 offsSz: 2533216 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 52776 numLines: 52776 ebwtTotLen: 3377664 ebwtTotSz: 3377664 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10