Settings: Output files: "/scratch/8793061.1.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/8793061.1.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: 2784462 Using parameters --bmax 2088347 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2088347 --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 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: 1.59112e+06 (target: 2088346) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (2088347) 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 1629310 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1629311 Getting block 2 of 7 Reserving size (2088347) 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 1114340 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1114341 Getting block 3 of 7 Reserving size (2088347) 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 2027011 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2027012 Getting block 4 of 7 Reserving size (2088347) 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 1518515 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1518516 Getting block 5 of 7 Reserving size (2088347) 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 1741852 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1741853 Getting block 6 of 7 Reserving size (2088347) 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 1190446 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1190447 Getting block 7 of 7 Reserving size (2088347) 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 1916370 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1916371 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2769678 fchr[G]: 5558384 fchr[T]: 8342567 fchr[$]: 11137850 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22935084 bytes to primary EBWT file: /scratch/8793061.1.linga/tophat2/tmp/segment_juncs.1.bt2 Wrote 2784468 bytes to secondary EBWT file: /scratch/8793061.1.linga/tophat2/tmp/segment_juncs.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11137850 bwtLen: 11137851 sz: 2784463 bwtSz: 2784463 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 696116 offsSz: 2784464 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58010 numLines: 58010 ebwtTotLen: 3712640 ebwtTotSz: 3712640 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:00:09 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: 2784462 Using parameters --bmax 2088347 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 2088347 --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 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 2; 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: 1.23754e+06 (target: 2088346) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (2088347) 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 1322606 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1322607 Getting block 2 of 9 Reserving size (2088347) 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 1281426 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1281427 Getting block 3 of 9 Reserving size (2088347) 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 1530487 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1530488 Getting block 4 of 9 Reserving size (2088347) 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 1089827 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1089828 Getting block 5 of 9 Reserving size (2088347) 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 1511988 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1511989 Getting block 6 of 9 Reserving size (2088347) 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 644242 (Using difference cover) Sorting block time: 00:00:00 Returning block of 644243 Getting block 7 of 9 Reserving size (2088347) 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 1565105 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1565106 Getting block 8 of 9 Reserving size (2088347) 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 894089 (Using difference cover) Sorting block time: 00:00:01 Returning block of 894090 Getting block 9 of 9 Reserving size (2088347) 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 1298072 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1298073 Exited Ebwt loop fchr[A]: 0 fchr[C]: 2769678 fchr[G]: 5558384 fchr[T]: 8342567 fchr[$]: 11137850 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 22935084 bytes to primary EBWT file: /scratch/8793061.1.linga/tophat2/tmp/segment_juncs.rev.1.bt2 Wrote 2784468 bytes to secondary EBWT file: /scratch/8793061.1.linga/tophat2/tmp/segment_juncs.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 11137850 bwtLen: 11137851 sz: 2784463 bwtSz: 2784463 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 696116 offsSz: 2784464 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 58010 numLines: 58010 ebwtTotLen: 3712640 ebwtTotSz: 3712640 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:00:11