Settings: Output files: "/scratch/9328372.1.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/9328372.1.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: 00:00:01 bmax according to bmaxDivN setting: 6072340 Using parameters --bmax 4554255 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4554255 --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: 00:00:02 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: 3.03617e+06 (target: 4554254) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (4554255) 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 2770001 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2770002 Getting block 2 of 8 Reserving size (4554255) 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 3627840 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3627841 Getting block 3 of 8 Reserving size (4554255) 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 3985333 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3985334 Getting block 4 of 8 Reserving size (4554255) 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 962402 (Using difference cover) Sorting block time: 00:00:00 Returning block of 962403 Getting block 5 of 8 Reserving size (4554255) 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 4381454 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4381455 Getting block 6 of 8 Reserving size (4554255) 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 2988446 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2988447 Getting block 7 of 8 Reserving size (4554255) 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 3010905 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3010906 Getting block 8 of 8 Reserving size (4554255) 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 2562972 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2562973 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6019035 fchr[G]: 12145245 fchr[T]: 18250397 fchr[$]: 24289360 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 43694577 bytes to primary EBWT file: /scratch/9328372.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 6072348 bytes to secondary EBWT file: /scratch/9328372.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 24289360 bwtLen: 24289361 sz: 6072340 bwtSz: 6072341 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1518086 offsSz: 6072344 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 126508 numLines: 126508 ebwtTotLen: 8096512 ebwtTotSz: 8096512 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:30 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: 6072340 Using parameters --bmax 4554255 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4554255 --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: 00:00:01 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: 3.46991e+06 (target: 4554254) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (4554255) 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 3390251 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3390252 Getting block 2 of 7 Reserving size (4554255) 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 3646477 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3646478 Getting block 3 of 7 Reserving size (4554255) 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 2814721 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2814722 Getting block 4 of 7 Reserving size (4554255) 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 4287440 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4287441 Getting block 5 of 7 Reserving size (4554255) 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 3301087 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3301088 Getting block 6 of 7 Reserving size (4554255) 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 4421245 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4421246 Getting block 7 of 7 Reserving size (4554255) 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 2428133 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2428134 Exited Ebwt loop fchr[A]: 0 fchr[C]: 6019035 fchr[G]: 12145245 fchr[T]: 18250397 fchr[$]: 24289360 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 43694577 bytes to primary EBWT file: /scratch/9328372.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 6072348 bytes to secondary EBWT file: /scratch/9328372.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 24289360 bwtLen: 24289361 sz: 6072340 bwtSz: 6072341 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1518086 offsSz: 6072344 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 126508 numLines: 126508 ebwtTotLen: 8096512 ebwtTotSz: 8096512 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:28