Settings: Output files: "/scratch/9351458.1.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/9351458.1.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: 4605689 Using parameters --bmax 3454267 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3454267 --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 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: 00:00:00 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 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: 2.30284e+06 (target: 3454266) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3454267) 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 1099369 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1099370 Getting block 2 of 8 Reserving size (3454267) 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 2410261 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2410262 Getting block 3 of 8 Reserving size (3454267) 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 3210948 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3210949 Getting block 4 of 8 Reserving size (3454267) 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 1853105 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1853106 Getting block 5 of 8 Reserving size (3454267) 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 3289677 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3289678 Getting block 6 of 8 Reserving size (3454267) 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 2680541 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2680542 Getting block 7 of 8 Reserving size (3454267) 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 1770143 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1770144 Getting block 8 of 8 Reserving size (3454267) 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 2108706 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2108707 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4583411 fchr[G]: 9240592 fchr[T]: 13793627 fchr[$]: 18422757 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 34154526 bytes to primary EBWT file: /scratch/9351458.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 4605696 bytes to secondary EBWT file: /scratch/9351458.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18422757 bwtLen: 18422758 sz: 4605690 bwtSz: 4605690 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1151423 offsSz: 4605692 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 95952 numLines: 95952 ebwtTotLen: 6140928 ebwtTotSz: 6140928 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: 4605689 Using parameters --bmax 3454267 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 3454267 --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 Avg bucket size: 2.30284e+06 (target: 3454266) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (3454267) 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 1889024 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1889025 Getting block 2 of 8 Reserving size (3454267) 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 2604291 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2604292 Getting block 3 of 8 Reserving size (3454267) 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 2409409 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2409410 Getting block 4 of 8 Reserving size (3454267) 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 2987895 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2987896 Getting block 5 of 8 Reserving size (3454267) 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 2946455 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2946456 Getting block 6 of 8 Reserving size (3454267) 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 1385301 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1385302 Getting block 7 of 8 Reserving size (3454267) 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 3200058 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3200059 Getting block 8 of 8 Reserving size (3454267) 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 1000317 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1000318 Exited Ebwt loop fchr[A]: 0 fchr[C]: 4583411 fchr[G]: 9240592 fchr[T]: 13793627 fchr[$]: 18422757 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 34154526 bytes to primary EBWT file: /scratch/9351458.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 4605696 bytes to secondary EBWT file: /scratch/9351458.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 18422757 bwtLen: 18422758 sz: 4605690 bwtSz: 4605690 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 1151423 offsSz: 4605692 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 95952 numLines: 95952 ebwtTotLen: 6140928 ebwtTotSz: 6140928 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:10