Settings: Output files: "/scratch/5574194.1.c/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/5574194.1.c/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: 2803075 Using parameters --bmax 2102307 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2102307 --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: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.60176e+06 (target: 2102306) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2102307) 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 2067060 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2067061 Getting block 2 of 7 Reserving size (2102307) 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 1122073 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1122074 Getting block 3 of 7 Reserving size (2102307) 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 2099056 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2099057 Getting block 4 of 7 Reserving size (2102307) 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 835315 (Using difference cover) Sorting block time: 00:00:00 Returning block of 835316 Getting block 5 of 7 Reserving size (2102307) 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 1755284 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1755285 Getting block 6 of 7 Reserving size (2102307) 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 1300122 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1300123 Getting block 7 of 7 Reserving size (2102307) 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 2033384 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2033385 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2791113 fchr[G]: 5599429 fchr[T]: 8409941 fchr[$]: 11212300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23061028 bytes to primary EBWT file: /scratch/5574194.1.c/tophat2/tmp/segment_juncs.1.bt2 Wrote 2803080 bytes to secondary EBWT file: /scratch/5574194.1.c/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11212300 bwtLen: 11212301 sz: 2803075 bwtSz: 2803076 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 700769 offsSz: 2803076 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58398 numLines: 58398 ebwtTotLen: 3737472 ebwtTotSz: 3737472 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:05 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: 00:00:00 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 2803075 Using parameters --bmax 2102307 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2102307 --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: 00:00:00 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: 1.24581e+06 (target: 2102306) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2102307) 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 772402 (Using difference cover) Sorting block time: 00:00:00 Returning block of 772403 Getting block 2 of 9 Reserving size (2102307) 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 1399491 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1399492 Getting block 3 of 9 Reserving size (2102307) 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 900096 (Using difference cover) Sorting block time: 00:00:00 Returning block of 900097 Getting block 4 of 9 Reserving size (2102307) 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 1693903 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1693904 Getting block 5 of 9 Reserving size (2102307) 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 855624 (Using difference cover) Sorting block time: 00:00:00 Returning block of 855625 Getting block 6 of 9 Reserving size (2102307) 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 2030195 (Using difference cover) Sorting block time: 00:00:00 Returning block of 2030196 Getting block 7 of 9 Reserving size (2102307) 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 946300 (Using difference cover) Sorting block time: 00:00:00 Returning block of 946301 Getting block 8 of 9 Reserving size (2102307) 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 1810580 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1810581 Getting block 9 of 9 Reserving size (2102307) 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 803701 (Using difference cover) Sorting block time: 00:00:01 Returning block of 803702 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2791113 fchr[G]: 5599429 fchr[T]: 8409941 fchr[$]: 11212300 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 23061028 bytes to primary EBWT file: /scratch/5574194.1.c/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2803080 bytes to secondary EBWT file: /scratch/5574194.1.c/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11212300 bwtLen: 11212301 sz: 2803075 bwtSz: 2803076 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 700769 offsSz: 2803076 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58398 numLines: 58398 ebwtTotLen: 3737472 ebwtTotSz: 3737472 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:06