Settings: Output files: "/scratch/8792848.1.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/8792848.1.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: 00:00:00 bmax according to bmaxDivN setting: 3110525 Using parameters --bmax 2332894 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2332894 --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: 00:00:01 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: 1.77744e+06 (target: 2332893) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2332894) 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 1945781 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1945782 Getting block 2 of 7 Reserving size (2332894) 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 1455715 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1455716 Getting block 3 of 7 Reserving size (2332894) 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 2216857 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2216858 Getting block 4 of 7 Reserving size (2332894) 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 1997344 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1997345 Getting block 5 of 7 Reserving size (2332894) 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 1843641 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1843642 Getting block 6 of 7 Reserving size (2332894) 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 1174172 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1174173 Getting block 7 of 7 Reserving size (2332894) 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 1808584 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1808585 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3120188 fchr[G]: 6206216 fchr[T]: 9268067 fchr[$]: 12442100 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 25101710 bytes to primary EBWT file: /scratch/8792848.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 3110532 bytes to secondary EBWT file: /scratch/8792848.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 12442100 bwtLen: 12442101 sz: 3110525 bwtSz: 3110526 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 777632 offsSz: 3110528 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 64803 numLines: 64803 ebwtTotLen: 4147392 ebwtTotSz: 4147392 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:14 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: 3110525 Using parameters --bmax 2332894 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2332894 --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 Avg bucket size: 1.38245e+06 (target: 2332893) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2332894) 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 87488 (Using difference cover) Sorting block time: 00:00:00 Returning block of 87489 Getting block 2 of 9 Reserving size (2332894) 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 2317478 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2317479 Getting block 3 of 9 Reserving size (2332894) 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 1593611 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1593612 Getting block 4 of 9 Reserving size (2332894) 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 782439 (Using difference cover) Sorting block time: 00:00:00 Returning block of 782440 Getting block 5 of 9 Reserving size (2332894) 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 1997336 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1997337 Getting block 6 of 9 Reserving size (2332894) 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 1544841 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1544842 Getting block 7 of 9 Reserving size (2332894) 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 820774 (Using difference cover) Sorting block time: 00:00:01 Returning block of 820775 Getting block 8 of 9 Reserving size (2332894) 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 2326135 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2326136 Getting block 9 of 9 Reserving size (2332894) 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 971990 (Using difference cover) Sorting block time: 00:00:00 Returning block of 971991 Exited Ebwt loop fchr[A]: 0 fchr[C]: 3120188 fchr[G]: 6206216 fchr[T]: 9268067 fchr[$]: 12442100 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 25101710 bytes to primary EBWT file: /scratch/8792848.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 3110532 bytes to secondary EBWT file: /scratch/8792848.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 12442100 bwtLen: 12442101 sz: 3110525 bwtSz: 3110526 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 777632 offsSz: 3110528 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 64803 numLines: 64803 ebwtTotLen: 4147392 ebwtTotSz: 4147392 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:12